Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_084935517.1 HA51_RS15475 trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase
Query= BRENDA::P09546 (1320 letters) >NCBI__GCF_002095475.1:WP_084935517.1 Length = 1314 Score = 2135 bits (5533), Expect = 0.0 Identities = 1077/1320 (81%), Positives = 1184/1320 (89%), Gaps = 6/1320 (0%) Query: 1 MGTTTMGVKLDDATRERIKSAATRIDRTPHWLIKQAIFSYLEQLENSDTLPELPALLSGA 60 MGTTTMGVKLD+ATR+RIK AA +IDRTPHWLIKQAIF+YL QLE + LPE+ L+ A Sbjct: 1 MGTTTMGVKLDEATRDRIKLAAGKIDRTPHWLIKQAIFNYLSQLEAGEGLPEISVQLADA 60 Query: 61 ANESDEAPTPAEEPHQPFLDFAEQILPQSVSRAAITAAYRRPETEAVSMLLEQARLPQPV 120 A+E + AP +E QPFLDFAE ILPQSV+R+AITAA+RRPET+AV MLLEQARLP P+ Sbjct: 61 ASE-EGAP---DESFQPFLDFAEHILPQSVTRSAITAAWRRPETDAVPMLLEQARLPAPL 116 Query: 121 AEQAHKLAYQLADKLRNQKNASGRAGMVQGLLQEFSLSSQEGVALMCLAEALLRIPDKAT 180 AE+ H+LAY LADKLR+QK A+GRAGMVQ LLQEFSLSSQEGVALMCLAEALLRIPDK T Sbjct: 117 AEKTHQLAYSLADKLRHQKGATGRAGMVQSLLQEFSLSSQEGVALMCLAEALLRIPDKPT 176 Query: 181 RDALIRDKISNGNWQSHIGRSPSLFVNAATWGLLFTGKLVSTHNEASLSRSLNRIIGKSG 240 RDALIRDKISNGNWQSH+GRSPS+FVNAATWGLLFTG+LVSTHNEA+LSRSLNRIIGKSG Sbjct: 177 RDALIRDKISNGNWQSHLGRSPSMFVNAATWGLLFTGRLVSTHNEANLSRSLNRIIGKSG 236 Query: 241 EPLIRKGVDMAMRLMGEQFVTGETIAEALANARKLEEKGFRYSYDMLGEAALTAADAQAY 300 EPLIRKGVDMAMRLMGEQFVTGETIAEALANARKLEEKGFRYSYDMLGEAALTA+DA+AY Sbjct: 237 EPLIRKGVDMAMRLMGEQFVTGETIAEALANARKLEEKGFRYSYDMLGEAALTASDAKAY 296 Query: 301 MVSYQQAIHAIGKASNGRGIYEGPGISIKLSALHPRYSRAQYDRVMEELYPRLKSLTLLA 360 ++SYQQAIHAIGKASNGRGIYEGPGISIKLSALHPRYSRAQY+RVMEELYP LKSLTLLA Sbjct: 297 LLSYQQAIHAIGKASNGRGIYEGPGISIKLSALHPRYSRAQYERVMEELYPILKSLTLLA 356 Query: 361 RQYDIGINIDAEESDRLEISLDLLEKLCFEPELAGWNGIGFVIQAYQKRCPLVIDYLIDL 420 R YDIGINIDAEE+DRLE+SLDLLEKLCFEPEL GWNGIGFVIQAY KRCP VID L+DL Sbjct: 357 RSYDIGINIDAEEADRLELSLDLLEKLCFEPELEGWNGIGFVIQAYMKRCPFVIDSLVDL 416 Query: 421 ATRSRRRLMIRLVKGAYWDSEIKRAQMDGLEGYPVYTRKVYTDVSYLACAKKLLAVPNLI 480 A RSRRRLMIRLVKGAYWDSEIKRAQ++GLEGYPVYTRKVYTD+SYLACA+KLLAVPNLI Sbjct: 417 AQRSRRRLMIRLVKGAYWDSEIKRAQVEGLEGYPVYTRKVYTDISYLACARKLLAVPNLI 476 Query: 481 YPQFATHNAHTLAAIYQLAGQNYYPGQYEFQCLHGMGEPLYEQVTGKVADGKLNRPCRIY 540 YPQFATHNAHTLAAIYQLAG NYYPGQYEFQCLHGMGEPLYEQV GKVADGKLNRPCRIY Sbjct: 477 YPQFATHNAHTLAAIYQLAGNNYYPGQYEFQCLHGMGEPLYEQVVGKVADGKLNRPCRIY 536 Query: 541 APVGTHETLLAYLVRRLLENGANTSFVNRIADTSLPLDELVADPVTAVEKLAQQEGQTGL 600 APVGTHETLLAYLVRRLLENGANTSFVNRIAD +LPLDELVADPVTAVEK+ EG GL Sbjct: 537 APVGTHETLLAYLVRRLLENGANTSFVNRIADNTLPLDELVADPVTAVEKMGASEGAVGL 596 Query: 601 PHPKIPLPRDLYGHGRDNSAGLDLANEHRLASLSSALLNSALQKWQALPMLEQPVAAGEM 660 PHPKIPLPR+LYG R NSAGLD+ANEHRLASLSSALLNSA Q W A P++E + G Sbjct: 597 PHPKIPLPRELYGEKRVNSAGLDMANEHRLASLSSALLNSASQPWIAQPLVEGALGEGVS 656 Query: 661 SPVINPAEPKDIVGYVREATPREVEQALESAVNNAPIWFATPPAERAAILHRAAVLMESQ 720 PV+NP+ P D+VG VREA+ EV +AL++AVN PIWFATPP ERAAIL RAA ME Q Sbjct: 657 RPVLNPSAPADVVGSVREASEAEVSEALDAAVNAGPIWFATPPQERAAILERAAEAMEGQ 716 Query: 721 MQQLIGILVREAGKTFSNAIAEVREAVDFLHYYAGQVRDDFANETHRPLGPVVCISPWNF 780 MQQLIG+LVREAGKT++NAIAEVREAVDFL+YYAG VRDDF NETHRPLGPVVCISPWNF Sbjct: 717 MQQLIGLLVREAGKTYNNAIAEVREAVDFLYYYAGMVRDDFDNETHRPLGPVVCISPWNF 776 Query: 781 PLAIFTGQIAAALAAGNSVLAKPAEQTPLIAAQGIAILLEAGVPPGVVQLLPGRGETVGA 840 PLAIF GQIAAALAAGNSVLAKPAEQTPLIAAQ + I+L+AGVP GV+QLLPG+GETVGA Sbjct: 777 PLAIFAGQIAAALAAGNSVLAKPAEQTPLIAAQAVQIMLDAGVPAGVLQLLPGQGETVGA 836 Query: 841 QLTGDDRVRGVMFTGSTEVATLLQRNIASRLDAQGRPIPLIAETGGMNAMIVDSSALTEQ 900 QLTGD+RVRGVMFTGST VATLLQRN+A RLD QGRP PLIAETGGMNAMIVDSSALTEQ Sbjct: 837 QLTGDERVRGVMFTGSTAVATLLQRNLAGRLDPQGRPTPLIAETGGMNAMIVDSSALTEQ 896 Query: 901 VVVDVLASAFDSAGQRCSALRVLCLQDEIADHTLKMLRGAMAECRMGNPGRLTTDIGPVI 960 VV+D++ASAFDSAGQRCSALR+LC+QD++ADHTLKMLRGAMAECRMGNP RL+TDIGPVI Sbjct: 897 VVIDIVASAFDSAGQRCSALRLLCVQDDVADHTLKMLRGAMAECRMGNPERLSTDIGPVI 956 Query: 961 DSEAKANIERHIQTMRSKGRPVFQAVRENSEDAREWQSGTFVAPTLIELDDFAELQKEVF 1020 D+EAK NI+RHIQ MR+KG V+QA ++N +D++EW SGTF+ PTLIELD ++L KEVF Sbjct: 957 DAEAKDNIDRHIQAMRNKGFTVYQAAQDNPQDSKEWNSGTFIKPTLIELDQVSDLDKEVF 1016 Query: 1021 GPVLHVVRYNRNQLPELIEQINASGYGLTLGVHTRIDETIAQVTGSAHVGNLYVNRNMVG 1080 GPVLHVVR+ RN LP+LI+QINASGYGLTLGVHTRIDETIAQVT A VGNLYVNRNMVG Sbjct: 1017 GPVLHVVRFARNSLPQLIDQINASGYGLTLGVHTRIDETIAQVTAGAKVGNLYVNRNMVG 1076 Query: 1081 AVVGVQPFGGEGLSGTGPKAGGPLYLYRLLANRPESALAVTLARQDAKYPVDAQLKAALT 1140 AVVGVQPFGGEGLSGTGPKAGGPLYLYRLL+NRP+ AL T RQDA+ PVD+ ++ L Sbjct: 1077 AVVGVQPFGGEGLSGTGPKAGGPLYLYRLLSNRPDGALRKTFDRQDAERPVDSSVRTELM 1136 Query: 1141 QPLNALREWAANRPELQALCTQYGELAQAGTQRLLPGPTGERNTWTLLPRERVLCIADDE 1200 AL+ WA ++P+L ALC +Y ELAQAGT R+LPGPTGERNT+TLLPRE VLCIAD+E Sbjct: 1137 SAHQALQTWAQDKPDLLALCQRYDELAQAGTVRVLPGPTGERNTFTLLPREHVLCIADNE 1196 Query: 1201 QDALTQLAAVLAVGSQVLWPDDALHRQLVKALPSAVSERIQLAKAENITAQPFDAVIFHG 1260 QDALTQLAAV +VGS LW DD LHR+L LP+AV R+ L K ++ A FDAVI+HG Sbjct: 1197 QDALTQLAAVTSVGSSALWQDDELHRELRTRLPAAVQPRVVLVK--DVLAADFDAVIYHG 1254 Query: 1261 DSDQLRALCEAVAARDGTIVSVQGFARGESNILLERLYIERSLSVNTAAAGGNASLMTIG 1320 D+DQLR LCE VAARDG IVSVQGFARGE+N+LLERL IERSLSVNTAAAGGNASLMTIG Sbjct: 1255 DADQLRTLCEQVAARDGAIVSVQGFARGETNLLLERLLIERSLSVNTAAAGGNASLMTIG 1314 Lambda K H 0.318 0.133 0.384 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 4461 Number of extensions: 171 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 1320 Length of database: 1314 Length adjustment: 48 Effective length of query: 1272 Effective length of database: 1266 Effective search space: 1610352 Effective search space used: 1610352 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 59 (27.3 bits)
Align candidate WP_084935517.1 HA51_RS15475 (trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase)
to HMM TIGR01238 (delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR01238.hmm # target sequence database: /tmp/gapView.2446148.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01238 [M=500] Accession: TIGR01238 Description: D1pyr5carbox3: delta-1-pyrroline-5-carboxylate dehydrogenase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-251 821.6 0.4 1.1e-251 821.6 0.4 1.4 2 NCBI__GCF_002095475.1:WP_084935517.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002095475.1:WP_084935517.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 821.6 0.4 1.1e-251 1.1e-251 1 499 [. 606 1109 .. 606 1110 .. 0.99 2 ? -4.3 0.4 0.24 0.24 291 328 .. 1239 1278 .. 1236 1280 .. 0.69 Alignments for each domain: == domain 1 score: 821.6 bits; conditional E-value: 1.1e-251 TIGR01238 1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvsea 71 +lyge r ns+G+d+ane++l+sl++ ll++a + + a p+v e a eg +pv np + d+vG v+ea NCBI__GCF_002095475.1:WP_084935517.1 606 ELYGEKRVNSAGLDMANEHRLASLSSALLNSASQPWIAQPLV-EGALGEGVSRPVLNPSAPADVVGSVREA 675 79****************************************.88999*********************** PP TIGR01238 72 daaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdfl 142 ++aev+ea+d+av+a ++w+at+++eraailer+a+ +e +m +l++llvreaGkt +naiaevreavdfl NCBI__GCF_002095475.1:WP_084935517.1 676 SEAEVSEALDAAVNAGPIWFATPPQERAAILERAAEAMEGQMQQLIGLLVREAGKTYNNAIAEVREAVDFL 746 *********************************************************************** PP TIGR01238 143 ryyakqvedvldeesakalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqea 213 yya+ v+d++d+e++++lG+vvcispwnfplaif GqiaaalaaGn+v+akpaeqt+liaa+av+++++a NCBI__GCF_002095475.1:WP_084935517.1 747 YYYAGMVRDDFDNETHRPLGPVVCISPWNFPLAIFAGQIAAALAAGNSVLAKPAEQTPLIAAQAVQIMLDA 817 *********************************************************************** PP TIGR01238 214 GvpagviqllpGrGedvGaaltsderiaGviftGstevarlinkalakredap...vpliaetGGqnamiv 281 Gvpagv+qllpG+Ge+vGa lt der++Gv+ftGst+va+l++++la r d++ +pliaetGG+namiv NCBI__GCF_002095475.1:WP_084935517.1 818 GVPAGVLQLLPGQGETVGAQLTGDERVRGVMFTGSTAVATLLQRNLAGRLDPQgrpTPLIAETGGMNAMIV 888 ***************************************************99999*************** PP TIGR01238 282 dstalaeqvvadvlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidae 352 ds+al+eqvv+d++asafdsaGqrcsalr+lcvq+dvad++l++++Gam e+++g+p+rl td+Gpvidae NCBI__GCF_002095475.1:WP_084935517.1 889 DSSALTEQVVIDIVASAFDSAGQRCSALRLLCVQDDVADHTLKMLRGAMAECRMGNPERLSTDIGPVIDAE 959 *********************************************************************** PP TIGR01238 353 akqnllahiekmkakakkvaqvkledd...vesekgtfvaptlfelddldelkkevfGpvlhvvrykadel 420 ak+n+ +hi++m++k+ +v+q+ +++ +e++ gtf++ptl+eld++++l+kevfGpvlhvvr+ ++ l NCBI__GCF_002095475.1:WP_084935517.1 960 AKDNIDRHIQAMRNKGFTVYQAAQDNPqdsKEWNSGTFIKPTLIELDQVSDLDKEVFGPVLHVVRFARNSL 1030 **********************9987544599*************************************** PP TIGR01238 421 dkvvdkinakGygltlGvhsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGply 491 +++d+ina+GygltlGvh+ri+et++q++ akvGn+yvnrn+vGavvGvqpfGGeGlsGtGpkaGGply NCBI__GCF_002095475.1:WP_084935517.1 1031 PQLIDQINASGYGLTLGVHTRIDETIAQVTAGAKVGNLYVNRNMVGAVVGVQPFGGEGLSGTGPKAGGPLY 1101 *********************************************************************** PP TIGR01238 492 lyrltrvr 499 lyrl++ r NCBI__GCF_002095475.1:WP_084935517.1 1102 LYRLLSNR 1109 ****9865 PP == domain 2 score: -4.3 bits; conditional E-value: 0.24 TIGR01238 291 vadvlasafdsaGqrcsa..lrvlcvqedvadrvltlikG 328 v+dvla+ fd+ a lr lc q d + ++G NCBI__GCF_002095475.1:WP_084935517.1 1239 VKDVLAADFDAVIYHGDAdqLRTLCEQVAARDGAIVSVQG 1278 7899999999987766553377777776666666665555 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (500 nodes) Target sequences: 1 (1314 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 47.88 // [ok]
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory