Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate AZOBR_RS23695 AZOBR_RS23695 transcriptional regulator
Query= reanno::azobra:AZOBR_RS23695 (1235 letters) >FitnessBrowser__azobra:AZOBR_RS23695 Length = 1235 Score = 2414 bits (6255), Expect = 0.0 Identities = 1235/1235 (100%), Positives = 1235/1235 (100%) Query: 1 IDTRTAPPSAAPGEAAPFADFAPPIRPATELRAAITAAYRRPEPECLPFLFEQASLPPGV 60 IDTRTAPPSAAPGEAAPFADFAPPIRPATELRAAITAAYRRPEPECLPFLFEQASLPPGV Sbjct: 1 IDTRTAPPSAAPGEAAPFADFAPPIRPATELRAAITAAYRRPEPECLPFLFEQASLPPGV 60 Query: 61 ITAAAATARKLITALRAKPRGRGVEGLIHEYSLSSQEGMALMCLAEALLRIPDHATRDAL 120 ITAAAATARKLITALRAKPRGRGVEGLIHEYSLSSQEGMALMCLAEALLRIPDHATRDAL Sbjct: 61 ITAAAATARKLITALRAKPRGRGVEGLIHEYSLSSQEGMALMCLAEALLRIPDHATRDAL 120 Query: 121 IRDKIAGGDWQAHLGKGGSMFVNAATWGLLITGKLTSAGGEQALSSALTRLIARGGEPLI 180 IRDKIAGGDWQAHLGKGGSMFVNAATWGLLITGKLTSAGGEQALSSALTRLIARGGEPLI Sbjct: 121 IRDKIAGGDWQAHLGKGGSMFVNAATWGLLITGKLTSAGGEQALSSALTRLIARGGEPLI 180 Query: 181 RRGVDFAMRMMGEQFVTGQTIQEALTNARTMEAEGFRYSYDMLGEAALTAEDAARYYADY 240 RRGVDFAMRMMGEQFVTGQTIQEALTNARTMEAEGFRYSYDMLGEAALTAEDAARYYADY Sbjct: 181 RRGVDFAMRMMGEQFVTGQTIQEALTNARTMEAEGFRYSYDMLGEAALTAEDAARYYADY 240 Query: 241 VNAIHAIGTASAGRGVYEGPGISIKLSAIHPRYSRAQADRVMDELLPRVKALALLAKGYD 300 VNAIHAIGTASAGRGVYEGPGISIKLSAIHPRYSRAQADRVMDELLPRVKALALLAKGYD Sbjct: 241 VNAIHAIGTASAGRGVYEGPGISIKLSAIHPRYSRAQADRVMDELLPRVKALALLAKGYD 300 Query: 301 IGLNIDAEEADRLELSLDLMESLCFDPDLAGWNGIGFVVQAYGKRCPYVIDFLIDLARRS 360 IGLNIDAEEADRLELSLDLMESLCFDPDLAGWNGIGFVVQAYGKRCPYVIDFLIDLARRS Sbjct: 301 IGLNIDAEEADRLELSLDLMESLCFDPDLAGWNGIGFVVQAYGKRCPYVIDFLIDLARRS 360 Query: 361 GHRLMIRLVKGAYWDSEIKRAQLDGLPDFPVYTRKVYTDVSYVACARKLLAAPEAVFPQF 420 GHRLMIRLVKGAYWDSEIKRAQLDGLPDFPVYTRKVYTDVSYVACARKLLAAPEAVFPQF Sbjct: 361 GHRLMIRLVKGAYWDSEIKRAQLDGLPDFPVYTRKVYTDVSYVACARKLLAAPEAVFPQF 420 Query: 421 ATHNAQTLATIYEMAGSDFQVGKYEFQCLHGMGEPLYKEVVGPLKRPCRIYAPVGTHETL 480 ATHNAQTLATIYEMAGSDFQVGKYEFQCLHGMGEPLYKEVVGPLKRPCRIYAPVGTHETL Sbjct: 421 ATHNAQTLATIYEMAGSDFQVGKYEFQCLHGMGEPLYKEVVGPLKRPCRIYAPVGTHETL 480 Query: 481 LAYLVRRLLENGANSSFVNRIADPAVPVDELVADPVAVARAIAPTGAPHALIALPRNLYA 540 LAYLVRRLLENGANSSFVNRIADPAVPVDELVADPVAVARAIAPTGAPHALIALPRNLYA Sbjct: 481 LAYLVRRLLENGANSSFVNRIADPAVPVDELVADPVAVARAIAPTGAPHALIALPRNLYA 540 Query: 541 PERANSAGIDLSDETELARLSAALSASAEMTWTAAPLLADGERAGQAQPVRNPADRRDVV 600 PERANSAGIDLSDETELARLSAALSASAEMTWTAAPLLADGERAGQAQPVRNPADRRDVV Sbjct: 541 PERANSAGIDLSDETELARLSAALSASAEMTWTAAPLLADGERAGQAQPVRNPADRRDVV 600 Query: 601 GSVTEASEALVAEAFGHAVAAASAWAATPPEERAASLFRAADTMQERMPTLLGLIVREAG 660 GSVTEASEALVAEAFGHAVAAASAWAATPPEERAASLFRAADTMQERMPTLLGLIVREAG Sbjct: 601 GSVTEASEALVAEAFGHAVAAASAWAATPPEERAASLFRAADTMQERMPTLLGLIVREAG 660 Query: 661 KSLPNAIAEVREAIDFLRYYGAQVRDRFDNATHRPLGPVVCISPWNFPLAIFSGQIAAAL 720 KSLPNAIAEVREAIDFLRYYGAQVRDRFDNATHRPLGPVVCISPWNFPLAIFSGQIAAAL Sbjct: 661 KSLPNAIAEVREAIDFLRYYGAQVRDRFDNATHRPLGPVVCISPWNFPLAIFSGQIAAAL 720 Query: 721 AAGNPVLAKPAEETPLIAAEAVRILHAAGIPAGALQLLPGAGEVGAALVGHEAVRGVMFT 780 AAGNPVLAKPAEETPLIAAEAVRILHAAGIPAGALQLLPGAGEVGAALVGHEAVRGVMFT Sbjct: 721 AAGNPVLAKPAEETPLIAAEAVRILHAAGIPAGALQLLPGAGEVGAALVGHEAVRGVMFT 780 Query: 781 GSTEVARLIQRQLAGRLLPDGAPIPLIAETGGQNAMIVDSSALAEQVVGDVIASAFDSAG 840 GSTEVARLIQRQLAGRLLPDGAPIPLIAETGGQNAMIVDSSALAEQVVGDVIASAFDSAG Sbjct: 781 GSTEVARLIQRQLAGRLLPDGAPIPLIAETGGQNAMIVDSSALAEQVVGDVIASAFDSAG 840 Query: 841 QRCSALRILCLQEDVADRTLAMLKGAMRELRIGNPDRLAVDVGPVISEEARATIAAHIEA 900 QRCSALRILCLQEDVADRTLAMLKGAMRELRIGNPDRLAVDVGPVISEEARATIAAHIEA Sbjct: 841 QRCSALRILCLQEDVADRTLAMLKGAMRELRIGNPDRLAVDVGPVISEEARATIAAHIEA 900 Query: 901 MRAKGRNVEFLPLPAETADGTFIAPTVIEIGGIHELEREVFGPVLHVVRFHRDDLDALVD 960 MRAKGRNVEFLPLPAETADGTFIAPTVIEIGGIHELEREVFGPVLHVVRFHRDDLDALVD Sbjct: 901 MRAKGRNVEFLPLPAETADGTFIAPTVIEIGGIHELEREVFGPVLHVVRFHRDDLDALVD 960 Query: 961 SINATGYGLTFGLHTRIDATIERVTGRIGAGNVYVNRNTIGAVVGVQPFGGHGLSGTGPK 1020 SINATGYGLTFGLHTRIDATIERVTGRIGAGNVYVNRNTIGAVVGVQPFGGHGLSGTGPK Sbjct: 961 SINATGYGLTFGLHTRIDATIERVTGRIGAGNVYVNRNTIGAVVGVQPFGGHGLSGTGPK 1020 Query: 1021 AGGPLYLSRLLSRRPKGWLEFRGPDAARAAGLAYGEWLRAKGFTAEASRCAGYVARSAIG 1080 AGGPLYLSRLLSRRPKGWLEFRGPDAARAAGLAYGEWLRAKGFTAEASRCAGYVARSAIG Sbjct: 1021 AGGPLYLSRLLSRRPKGWLEFRGPDAARAAGLAYGEWLRAKGFTAEASRCAGYVARSAIG 1080 Query: 1081 GGAELNGPVGERNLYELHGRGRVLLLPQTRTGLLLQLGAVLATGNSAAVDAPPDLAELLR 1140 GGAELNGPVGERNLYELHGRGRVLLLPQTRTGLLLQLGAVLATGNSAAVDAPPDLAELLR Sbjct: 1081 GGAELNGPVGERNLYELHGRGRVLLLPQTRTGLLLQLGAVLATGNSAAVDAPPDLAELLR 1140 Query: 1141 GLPPALAARVRTTADWRDVGPLAAVLVEGDRERVTAINRRVADLPGPILLVQAATAEALA 1200 GLPPALAARVRTTADWRDVGPLAAVLVEGDRERVTAINRRVADLPGPILLVQAATAEALA Sbjct: 1141 GLPPALAARVRTTADWRDVGPLAAVLVEGDRERVTAINRRVADLPGPILLVQAATAEALA 1200 Query: 1201 AGRGEGYDLDLLLNERSVSVNTAAAGGNASLVAMS 1235 AGRGEGYDLDLLLNERSVSVNTAAAGGNASLVAMS Sbjct: 1201 AGRGEGYDLDLLLNERSVSVNTAAAGGNASLVAMS 1235 Lambda K H 0.319 0.136 0.396 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: 4391 Number of extensions: 160 Number of successful extensions: 1 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: 1235 Length of database: 1235 Length adjustment: 48 Effective length of query: 1187 Effective length of database: 1187 Effective search space: 1408969 Effective search space used: 1408969 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 59 (27.3 bits)
Align candidate AZOBR_RS23695 AZOBR_RS23695 (transcriptional regulator)
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.20797.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-234 764.1 0.8 4.2e-234 763.6 0.8 1.2 1 lcl|FitnessBrowser__azobra:AZOBR_RS23695 AZOBR_RS23695 transcriptional re Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS23695 AZOBR_RS23695 transcriptional regulator # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 763.6 0.8 4.2e-234 4.2e-234 1 498 [. 537 1033 .. 537 1035 .. 0.98 Alignments for each domain: == domain 1 score: 763.6 bits; conditional E-value: 4.2e-234 TIGR01238 1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGq 67 +ly+ r ns+G+dl+ e+el++l++ l ++a+ ++ aap++++ + g+aqpv+npadr+d+vG lcl|FitnessBrowser__azobra:AZOBR_RS23695 537 NLYAPERANSAGIDLSDETELARLSAALSASAEMTWTAAPLLADG-ERAGQAQPVRNPADRRDVVGS 602 589999************************************655.55699**************** PP TIGR01238 68 vseadaaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiae 134 v+ea++a v ea + avaa++ w at+++eraa l r+ad ++++mp+l++l+vreaGk+l naiae lcl|FitnessBrowser__azobra:AZOBR_RS23695 603 VTEASEALVAEAFGHAVAAASAWAATPPEERAASLFRAADTMQERMPTLLGLIVREAGKSLPNAIAE 669 ******************************************************************* PP TIGR01238 135 vreavdflryyakqvedvldeesakalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsl 201 vrea+dflryy+ qv+d +d+ ++++lG+vvcispwnfplaif GqiaaalaaGn v+akpae+t+l lcl|FitnessBrowser__azobra:AZOBR_RS23695 670 VREAIDFLRYYGAQVRDRFDNATHRPLGPVVCISPWNFPLAIFSGQIAAALAAGNPVLAKPAEETPL 736 ******************************************************************* PP TIGR01238 202 iaaravellqeaGvpagviqllpGrGedvGaaltsderiaGviftGstevarlinkalakredap.. 266 iaa+av +l+ aG+pag++qllpG+Ge vGaal +e+++Gv+ftGstevarli+++la r ++ lcl|FitnessBrowser__azobra:AZOBR_RS23695 737 IAAEAVRILHAAGIPAGALQLLPGAGE-VGAALVGHEAVRGVMFTGSTEVARLIQRQLAGRLLPDga 802 ***************************.*********************************865444 PP TIGR01238 267 .vpliaetGGqnamivdstalaeqvvadvlasafdsaGqrcsalrvlcvqedvadrvltlikGamde 332 +pliaetGGqnamivds+alaeqvv dv+asafdsaGqrcsalr+lc+qedvadr+l ++kGam e lcl|FitnessBrowser__azobra:AZOBR_RS23695 803 pIPLIAETGGQNAMIVDSSALAEQVVGDVIASAFDSAGQRCSALRILCLQEDVADRTLAMLKGAMRE 869 4****************************************************************** PP TIGR01238 333 lkvgkpirlttdvGpvidaeakqnllahiekmkakakkvaqvkleddvesekgtfvaptlfelddld 399 l++g+p rl dvGpvi +ea+ + ahie+m+ak+++v + l + e+ gtf+apt++e+ ++ lcl|FitnessBrowser__azobra:AZOBR_RS23695 870 LRIGNPDRLAVDVGPVISEEARATIAAHIEAMRAKGRNVEFLPLPA--ETADGTFIAPTVIEIGGIH 934 *******************************************999..999**************** PP TIGR01238 400 elkkevfGpvlhvvrykadeldkvvdkinakGygltlGvhsrieetvrqiekrakvGnvyvnrnlvG 466 el++evfGpvlhvvr+++d+ld +vd ina+Gyglt+G+h+ri+ t+ ++++r+ +Gnvyvnrn +G lcl|FitnessBrowser__azobra:AZOBR_RS23695 935 ELEREVFGPVLHVVRFHRDDLDALVDSINATGYGLTFGLHTRIDATIERVTGRIGAGNVYVNRNTIG 1001 ******************************************************************* PP TIGR01238 467 avvGvqpfGGeGlsGtGpkaGGplylyrltrv 498 avvGvqpfGG+GlsGtGpkaGGplyl rl++ lcl|FitnessBrowser__azobra:AZOBR_RS23695 1002 AVVGVQPFGGHGLSGTGPKAGGPLYLSRLLSR 1033 *****************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (500 nodes) Target sequences: 1 (1235 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 22.55 // [ok]
This GapMind analysis is from Sep 17 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