########################################
# Program: needle
# Rundate: Wed 30 May 2018 15:45:56
# Commandline: needle
#    -outfile /Users/teresatavella/Documents/models_new/seqid30_85/sp_P37871_RPOC_BACSU_1hqm_D/needle.txt
#    -asequence /Users/teresatavella/Documents/models_new/seqid30_85/sp_P37871_RPOC_BACSU_1hqm_D/sp_P37871_RPOC_BACSU_DNA-directed_RNA_polymerase_subunit_betaprime_OS_Bacillus_subtilis_strain_168_OX_224308_GN_rpoC_PE_1_SV_4.fa
#    -bsequence /Users/teresatavella/Documents/models_new/seqid30_85/sp_P37871_RPOC_BACSU_1hqm_D/1hqm_D.fa
#    -gapopen 10
#    -gapextend 0.5
# Align_format: srspair
# Report_file: /Users/teresatavella/Documents/models_new/seqid30_85/sp_P37871_RPOC_BACSU_1hqm_D/needle.txt
########################################

#=======================================
#
# Aligned_sequences: 2
# 1: sp_P37871_RPOC_BACSU_DNA-directed_RNA_polymerase_subunit_betaprime_OS_Bacillus_subtilis_strain_168_OX_224308_GN_rpoC_PE_1_SV_4
# 2: 1hqm_D_mol_protein_length_1265__DNA-directed_RNA_polymerase_subunit_beta'
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 1284
# Identity:     600/1284 (46.7%)
# Similarity:   799/1284 (62.2%)
# Gaps:         194/1284 (15.1%)
# Score: 2824.5
# 
#
#=======================================

sp_P37871_RPO      1 MLDVNNFEYMNIGLASPDKIRSWSFGEVKKPETINYRTLKPEKDGLFCER     50
                         .....:.|.||||:||||||:|||:||||                 
1hqm_D_mol_pr      1 ----KEVRKVRIALASPEKIRSWSYGEVEKPET-----------------     29

sp_P37871_RPO     51 IFGPTKDWECHCGKYKRVRYKGVVCDRCGVEVTRAKVRRERMGHIELAAP    100
                                         :|.||:||||||||:.|||.||||||||.|
1hqm_D_mol_pr     30 --------------------EGKVCERCGVEVTRSIVRRYRMGHIELATP     59

sp_P37871_RPO    101 VSHIWYFKGIPSRMGLVLDMSPRALEEVIYFASYVVTDPA-----NTPLE    145
                     .:|||:.|.:||::|.:||:....||:|:||..|:|.||.     ..|:|
1hqm_D_mol_pr     60 AAHIWFVKDVPSKIGTLLDLFATELEQVLYFNKYIVLDPKGAVLDGVPVE    109

sp_P37871_RPO    146 KKQLLSE-----------------------KEYRAYLDKYGNKFQASMGA    172
                     |:|||::                       ...............|.|||
1hqm_D_mol_pr    110 KRQLLTDXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXIDARMGA    159

sp_P37871_RPO    173 EAIHKLLQDIDLVKEVDMLKEELKTSQGQRRTRAIKRLEVLEAFRNSGNK    222
                     |||.:||:::||.|....|.||:|.....||.:|.|||||:.||.:|||:
1hqm_D_mol_pr    160 EAIQELLKELDLEKLERELLEEMKHPSRARRAKARKRLEVVRAFLDSGNR    209

sp_P37871_RPO    223 PSWMILDVLPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLL    272
                     |.||||:.:||:||:            |||||||||||:||||||||:||
1hqm_D_mol_pr    210 PEWMILEAVPVLPPD------------ATSDLNDLYRRLINRNNRLKKLL    247

sp_P37871_RPO    273 DLGAPSIIVQNEKRMLQEAVDALIDNGRRGRPVTGPGN-RPLKSLSHMLK    321
                     ..|||.||::||||||||||||:|||||||.|||.||: |||:||:.:|.
1hqm_D_mol_pr    248 AQGAPEIIIRNEKRMLQEAVDAVIDNGRRGSPVTNPGSERPLRSLTDILS    297

sp_P37871_RPO    322 GKQGRFRQNLLGKRVDYSGRSVIVVGPHLKMYQCGLPKEMALELFKPFVM    371
                     |||||||||||||||||||||||||||.||::||||||.|||||||||::
1hqm_D_mol_pr    298 GKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLL    347

sp_P37871_RPO    372 KELVEKGLAHNIKSAKRKIER---VQPEVWDVLESVIKEHPVLLNRAPTL    418
                     |::.||..|.|:|:|:|.:||   ::.||||.||.||....|||||||||
1hqm_D_mol_pr    348 KKMEEKAFAPNVKAARRMLERQRDIKDEVWDALEEVIHGKVVLLNRAPTL    397

sp_P37871_RPO    419 HRLGIQAFEPTLVEGRAIRLHPLVCTAYNADFDGDQMAVHVPLSAEAQAE    468
                     ||||||||:|.||||::|:||||||.|:||||||||||||||||:.||||
1hqm_D_mol_pr    398 HRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAE    447

sp_P37871_RPO    469 ARILMLAAQNILNPKDGKPVVTPSQDMVLGNYYLTLERAGAVGEGMVFKN    518
                     |||.||:|.|:|:|..|:|:..||:|::||.||:|..|....|.||.|..
1hqm_D_mol_pr    448 ARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGMAFAT    497

sp_P37871_RPO    519 TDEALLAYQNGYVHLHTRVAVAANS-----LKNV----------------    547
                     .:|||.||:.|.|.|:..:.||...     ||.|                
1hqm_D_mol_pr    498 PEEALAAYERGEVALNAPIVVAGRETSVGRLKFVFANPDEALLAVAHGLL    547

sp_P37871_RPO    548 ----TFTEEQRSKLLITTVGKLVFNEILPESFPYMNEPTKSNIEEKTPDR    593
                         |.|.....:.|.|..|:::|..|:.|:..          :||    
1hqm_D_mol_pr    548 DLQDTVTTRYLGRRLETNPGRILFARIVGEAVG----------DEK----    583

sp_P37871_RPO    594 FFLEKGADVKAVIAQQPI--NAPFKKGILGKIIAEIFKRFHITETSKMLD    641
                                 :||:.|  :.|.:|..|..::.:.|.|..:.:|:::||
1hqm_D_mol_pr    584 ------------VAQELIQMDVPQEKNSLKDLVYQAFLRLGMEKTARLLD    621

sp_P37871_RPO    642 RMKNLGFKYSTKAG-ITVGVSDIVVLDDKQEILEEAQSKVDNVMKQFRRG    690
                     .:|..||..||.:| ||:|:.|.|:.::||..||||..|:..:.:.:..|
1hqm_D_mol_pr    622 ALKYYGFTLSTTSGIITIGIDDAVIPEEKQRYLEEADRKLRQIEQAYEMG    671

sp_P37871_RPO    691 LITEEERYERVISIWSAAKDVIQGKLMKSLDE---LNPIYMMSDSGARGN    737
                     .:|:.|||::||.:|:...:.:...:..:.:|   .||:|:|:.||||||
1hqm_D_mol_pr    672 FLTDRERYDQVIQLWTETTEKVTQAVFNNFEENYPFNPLYVMAQSGARGN    721

sp_P37871_RPO    738 ASNFTQLAGMRGLMANPAGRIIELPIKSSFREGLTVLEYFISTHGARKGL    787
                     .....||.||||||..|:|...|:|::|||||||||||||||:||||||.
1hqm_D_mol_pr    722 PQQIRQLCGMRGLMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGG    771

sp_P37871_RPO    788 ADTALKTADSGYLTRRLVDVAQDVIIRETDCGTDRGILAKPL---KEGTE    834
                     |||||:|||||||||:|||||.::::||.||||.: .::.||   .|.|.
1hqm_D_mol_pr    772 ADTALRTADSGYLTRKLVDVAHEIVVREADCGTTK-YISVPLFQMDEVTR    820

sp_P37871_RPO    835 TIERLEER------LIGRFARKQV----KHPETGEVLVNENELIDEDKAL    874
                     |: ||.:|      |.||...::|    :..|.|..|    .|.|....:
1hqm_D_mol_pr    821 TL-RLRKRSDIESGLYGRVLAREVEALGRRLEEGRYL----SLEDVHFLI    865

sp_P37871_RPO    875 EIVEAG-IEEVWIRSAFTCNTPHGVCKRCYGRNLATGSDVEVGEAVGIIA    923
                     :..||| :.||.:||..||.|.:|||::|||.:|:....|.:|||||::|
1hqm_D_mol_pr    866 KAAEAGEVREVPVRSPLTCQTRYGVCQKCYGYDLSMARPVSIGEAVGVVA    915

sp_P37871_RPO    924 AQSIGEPGTQLTMRTFHTGGVAGDDITQGLPRIQELFEARNPKGQATITE    973
                     |:|||||||||||||       |.||||||||:.||||||.||.:|.|:|
1hqm_D_mol_pr    916 AESIGEPGTQLTMRT-------GTDITQGLPRVIELFEARRPKAKAVISE    958

sp_P37871_RPO    974 IDGTVVEINEVRDKQQEIVVQGAVETRSYTAPYNSRLKVAEGDKITRGQV   1023
                     ||| ||.|.|..|: ..:.|:....::.|..|.::||.|.:||.:..||.
1hqm_D_mol_pr    959 IDG-VVRIEEGEDR-LSVFVESEGFSKEYKLPKDARLLVKDGDYVEAGQP   1006

sp_P37871_RPO   1024 LTEGSIDPKELLKVTDLTTVQEYLLHEVQKVYRMQGVEIGDKHVEVMVRQ   1073
                     ||.|:|||.:||:......|:.||:.|:|||||.|||::.|||:|::|||
1hqm_D_mol_pr   1007 LTRGAIDPHQLLEAKGPEAVERYLVDEIQKVYRAQGVKLHDKHIEIVVRQ   1056

sp_P37871_RPO   1074 MLRKVRVIDAGDTDVLPGTLLDIHQFTEANKKVLLEGNRPATGRPVLLGI   1123
                     ||:.|.|.|.||:.:|.|.:|:.......|::::..   |...:|:|:|:
1hqm_D_mol_pr   1057 MLKYVEVTDPGDSPLLEGQVLEKWDVEALNERLIAV---PVAWKPLLMGV   1103

sp_P37871_RPO   1124 TKASLETDSFLSAASFQETTRVLTDAAIKGKRDELLGLKENVIIGKLVPA   1173
                     ||::|.|.|:|||||||.||.|||:|||.||:|||:|||||||:|:|:||
1hqm_D_mol_pr   1104 TKSALSTKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPA   1153

sp_P37871_RPO   1174 GTG--------MMKYRKVKPVSNVQPTDDMVPVE   1199
                     |||        ::..|.:|.:.            
1hqm_D_mol_pr   1154 GTGSDFVRFTQVVDQRTLKAIE------------   1175


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