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)
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