########################################
# Program: needle
# Rundate: Wed 30 May 2018 14:48:53
# Commandline: needle
#    -outfile /Users/teresatavella/Documents/models_new/seqid30_85/sp_Q9RLT9_RPOB_LISMO_3iyd_C/needle.txt
#    -asequence /Users/teresatavella/Documents/models_new/seqid30_85/sp_Q9RLT9_RPOB_LISMO_3iyd_C/sp_Q9RLT9_RPOB_LISMO_DNA-directed_RNA_polymerase_subunit_beta_OS_Listeria_monocytogenes_serovar_12a_strain_ATCC_BAA-679__EGD-e_OX_169963_GN_rpoB_PE_3_SV_1.fa
#    -bsequence /Users/teresatavella/Documents/models_new/seqid30_85/sp_Q9RLT9_RPOB_LISMO_3iyd_C/3iyd_C.fa
#    -gapopen 10
#    -gapextend 0.5
# Align_format: srspair
# Report_file: /Users/teresatavella/Documents/models_new/seqid30_85/sp_Q9RLT9_RPOB_LISMO_3iyd_C/needle.txt
########################################

#=======================================
#
# Aligned_sequences: 2
# 1: sp_Q9RLT9_RPOB_LISMO_DNA-directed_RNA_polymerase_subunit_beta_OS_Listeria_monocytogenes_serovar_12a_strain_ATCC_BAA-679__EGD-e_OX_169963_GN_rpoB_PE_3_SV_1
# 2: 3iyd_C_mol_protein_length_1342__DNA-directed_RNA_polymerase_subunit_beta
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 1229
# Identity:     624/1229 (50.8%)
# Similarity:   816/1229 (66.4%)
# Gaps:         185/1229 (15.1%)
# Score: 3125.5
# 
#
#=======================================

sp_Q9RLT9_RPO      1 MSGHSGHDVKYGRHRTRRSFARISEVLELPNLIEIQTASYQWFLDE----     46
                                   |.|:.|.:..:||::|.|:.||..|:|.|:::    
3iyd_C_mol_pr      1 --------------RIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEG     36

sp_Q9RLT9_RPO     47 --GLREMFRDISPIEDFAGNLSLEFIDYDLGEPKYSVEESKNRDANYAAP     94
                       ||...||.:.||:.::||..|:::.|.||||.:.|:|.:.|...|:||
3iyd_C_mol_pr     37 QYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAP     86

sp_Q9RLT9_RPO     95 LRVKLRLI--NKETGE-----VKDQEVFMGDFPLMTEMGTFIINGAERVI    137
                     |||||||:  .:|..|     :|:|||:||:.||||:.|||:|||.||||
3iyd_C_mol_pr     87 LRVKLRLVIYEREAPEGTVKDIKEQEVYMGEIPLMTDNGTFVINGTERVI    136

sp_Q9RLT9_RPO    138 VSQLVRSPGVYFN---GKLDKNGKKGFGSTVIPNRGAWLEYETDAKDVVH    184
                     ||||.|||||:|:   ||...:||..:.:.:||.||:||::|.|.||.:.
3iyd_C_mol_pr    137 VSQLHRSPGVFFDSDKGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLF    186

sp_Q9RLT9_RPO    185 VRIDRTRKLPVTVLLRALGFGSDQ------EIIDLIG-------------    215
                     |||||.||||.|::||||.:.::|      |.:||:.             
3iyd_C_mol_pr    187 VRIDRRRKLPATIILRALNYTTEQILDLFFEKVDLLAKLSQSGHKRIETL    236

sp_Q9RLT9_RPO    216 -DND-----YLRNTLEKDNTDNAEKALLEIYERLRPGEPPTVDNARSLLV    259
                      .||     |:..||..|.|::...||:|||..:|||||||.:.|.||..
3iyd_C_mol_pr    237 FTNDLDHGPYISETLRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFE    286

sp_Q9RLT9_RPO    260 SRFFDPKRYDLASVGRYKINKKLHLKNRLFNQTLAETLVDPETGEIIASK    309
                     :.||...||||::|||.|.|:.|          |.|.:    .|..|.||
3iyd_C_mol_pr    287 NLFFSEDRYDLSAVGRMKFNRSL----------LREEI----EGSGILSK    322

sp_Q9RLT9_RPO    310 GDILDRRNLDQIIPNLENGVGFRTLRPTDGVMEDSVLVQSIKIYAPNDEE    359
                     .||:|                         ||:..:              
3iyd_C_mol_pr    323 DDIID-------------------------VMKKLI--------------    333

sp_Q9RLT9_RPO    360 KEINIIGNAYIEENVKHITPSDIISSISYFFNLLHGVGDTDDIDHLGNRR    409
                                                    ::.:|.|:.||||||||||
3iyd_C_mol_pr    334 -------------------------------DIRNGKGEVDDIDHLGNRR    352

sp_Q9RLT9_RPO    410 LRSVGELLQNQFRIGLSRMERVVRERMSIQDMTTITPQQLINIRPVVASI    459
                     :|||||:.:||||:||.|:||.|:||:|:.|:.|:.||.:||.:|:.|::
3iyd_C_mol_pr    353 IRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDMINAKPISAAV    402

sp_Q9RLT9_RPO    460 KEFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGGLTRERAGYEVRDVHY    509
                     |||||||||||||||.|||.|:|||||:||||||||||||||:||||||.
3iyd_C_mol_pr    403 KEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHP    452

sp_Q9RLT9_RPO    510 SHYGRMCPIETPEGPNIGLINSLSSFAKVNKFGFIETPYRRVDPETNRVT    559
                     :||||:||||||||||||||||||.:|:.|::||:|||||:|....  ||
3iyd_C_mol_pr    453 THYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGV--VT    500

sp_Q9RLT9_RPO    560 DKIDYLTADEEDNYVVAQANSKLDEQGTFTEEEVMARFRSENLAVEKERI    609
                     |:|.||:|.||.|||:|||||.|||:|.|.|:.|..|.:.|:....::::
3iyd_C_mol_pr    501 DEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQV    550

sp_Q9RLT9_RPO    610 DYMDVSPKQVVSVATACIPFLENDDSNRALMGANMQRQAVPLMHPEAPFV    659
                     ||||||.:|||||..:.|||||:||:|||||||||||||||.:..:.|.|
3iyd_C_mol_pr    551 DYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLV    600

sp_Q9RLT9_RPO    660 GTGMEHVSAKDSGAAVTAKHDGIVEHVEAREIWVRRVSLVDGKEV---TG    706
                     |||||...|.|||....||..|:|::|:|..|.::    |:..|:   ..
3iyd_C_mol_pr    601 GTGMERAVAVDSGVTAVAKRGGVVQYVDASRIVIK----VNEDEMYPGEA    646

sp_Q9RLT9_RPO    707 GIDKYTLRKFVRSNQGTCYNQRPNVAEGDRVVKGEILGNGPSMDSGELAL    756
                     |||.|.|.|:.||||.||.||.|.|:.|:.|.:|::|.:|||.|.|||||
3iyd_C_mol_pr    647 GIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELAL    696

sp_Q9RLT9_RPO    757 GRNVLVAFMTWDGYNYEDAIIMSERLVKDDVYTSIHIEEFESEARDTKLG    806
                     |:|:.||||.|:|||:||:|::|||:|::|.:|:|||:|....:||||||
3iyd_C_mol_pr    697 GQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLG    746

sp_Q9RLT9_RPO    807 PEEMTRDIPNVGEDALRDLDERGIIRVGAEVKDNDLLVGKVTPKGVTELT    856
                     |||:|.|||||||.||..|||.||:.:||||...|:|||||||||.|:||
3iyd_C_mol_pr    747 PEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLT    796

sp_Q9RLT9_RPO    857 AEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKIFTREAGD-ELPPG    905
                     .||:||.|||||||.:|:|:|||||:|..|.|:||::|||:..: :|.||
3iyd_C_mol_pr    797 PEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDLAPG    846

sp_Q9RLT9_RPO    906 VNQLVRVYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPFMPDGTPVD    955
                     |.::|:||:..||:|..|||||||||||||||:|.|.||||:..:|||||
3iyd_C_mol_pr    847 VLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVD    896

sp_Q9RLT9_RPO    956 IMLNPLGVPSRMNIGQVLELHLGMAARALGIHVATPVFDGANEEDVWSTV   1005
                     |:||||||||||||||:||.||||||:.:|:.:||||||||.|.::...:
3iyd_C_mol_pr    897 IVLNPLGVPSRMNIGQILETHLGMAAKGIGMPIATPVFDGAKEAEIKELL    946

sp_Q9RLT9_RPO   1006 EEAGMARDAKTILYDGRSGEAFDNRISVGVMYMIKLAHMVDDKLHARSTG   1055
                     :...:....:..|||||:||.|:..::||.|||:||.|:||||:||||||
3iyd_C_mol_pr    947 KLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTG    996

sp_Q9RLT9_RPO   1056 PYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTIKSDDVV   1105
                     .|||||||||||||||||||||||||||||||||||||||:||:|||||.
3iyd_C_mol_pr    997 SYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVN   1046

sp_Q9RLT9_RPO   1106 GRVKTYEAIVKGESVPEPGVPESFKVLIKELQSLGMDVKMLSADEEEIEM   1155
                     ||.|.|:.||.|....|||:||||.||:||::|||:::::    |:|   
3iyd_C_mol_pr   1047 GRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIEL----EDE---   1089

sp_Q9RLT9_RPO   1156 RDMDDDDFTNQNDAFNIVQPENAAAEKTE   1184
                                                  
3iyd_C_mol_pr   1089 -----------------------------   1089


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