Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate HSERO_RS00905 HSERO_RS00905 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase
Query= reanno::HerbieS:HSERO_RS00905 (1230 letters) >FitnessBrowser__HerbieS:HSERO_RS00905 Length = 1230 Score = 2408 bits (6241), Expect = 0.0 Identities = 1230/1230 (100%), Positives = 1230/1230 (100%) Query: 1 MTHVASAAVAAPFGGFQAELLPTPSPLRAAITAAYRRDEREAVQWLLQQVQEEQPWKDAT 60 MTHVASAAVAAPFGGFQAELLPTPSPLRAAITAAYRRDEREAVQWLLQQVQEEQPWKDAT Sbjct: 1 MTHVASAAVAAPFGGFQAELLPTPSPLRAAITAAYRRDEREAVQWLLQQVQEEQPWKDAT 60 Query: 61 QQLARKLVQQVREKRTRSSGVDALMHEFSLSSEEGVALMCLAEALLRIPDRQTADRLIAD 120 QQLARKLVQQVREKRTRSSGVDALMHEFSLSSEEGVALMCLAEALLRIPDRQTADRLIAD Sbjct: 61 QQLARKLVQQVREKRTRSSGVDALMHEFSLSSEEGVALMCLAEALLRIPDRQTADRLIAD 120 Query: 121 KISKGDWRKHLGESPSLFVNAATWGLLITGKLVSTSSESGLTQAITRLIGKGGEPLIRKG 180 KISKGDWRKHLGESPSLFVNAATWGLLITGKLVSTSSESGLTQAITRLIGKGGEPLIRKG Sbjct: 121 KISKGDWRKHLGESPSLFVNAATWGLLITGKLVSTSSESGLTQAITRLIGKGGEPLIRKG 180 Query: 181 VDLAMRMLGNQFVTGQTIEEALDNSRENEKRGYRYSYDMLGEAALTMHDADAYYQSYESA 240 VDLAMRMLGNQFVTGQTIEEALDNSRENEKRGYRYSYDMLGEAALTMHDADAYYQSYESA Sbjct: 181 VDLAMRMLGNQFVTGQTIEEALDNSRENEKRGYRYSYDMLGEAALTMHDADAYYQSYESA 240 Query: 241 IHAIGRASNGRGIKDGPGISVKLSALHPRYSRAQHARVMSELLPRLKQLLLLAKQYDIGL 300 IHAIGRASNGRGIKDGPGISVKLSALHPRYSRAQHARVMSELLPRLKQLLLLAKQYDIGL Sbjct: 241 IHAIGRASNGRGIKDGPGISVKLSALHPRYSRAQHARVMSELLPRLKQLLLLAKQYDIGL 300 Query: 301 NIDAEEADRLELSLDMMEVLVADPDLAGFDGLGFVVQGYQKRCPFVIDYLVDLARRNGRR 360 NIDAEEADRLELSLDMMEVLVADPDLAGFDGLGFVVQGYQKRCPFVIDYLVDLARRNGRR Sbjct: 301 NIDAEEADRLELSLDMMEVLVADPDLAGFDGLGFVVQGYQKRCPFVIDYLVDLARRNGRR 360 Query: 361 LMIRLVKGAYWDSEIKRAQVDGLEGYPVYTRKVHTDLSYLTCAQKLLAATDVIYPQFATH 420 LMIRLVKGAYWDSEIKRAQVDGLEGYPVYTRKVHTDLSYLTCAQKLLAATDVIYPQFATH Sbjct: 361 LMIRLVKGAYWDSEIKRAQVDGLEGYPVYTRKVHTDLSYLTCAQKLLAATDVIYPQFATH 420 Query: 421 NAHTLAAIYHWARQHQIDNYEFQCLHGMGETLYDQVVGPDNLGKACRVYAPVGSHQTLLA 480 NAHTLAAIYHWARQHQIDNYEFQCLHGMGETLYDQVVGPDNLGKACRVYAPVGSHQTLLA Sbjct: 421 NAHTLAAIYHWARQHQIDNYEFQCLHGMGETLYDQVVGPDNLGKACRVYAPVGSHQTLLA 480 Query: 481 YLVRRLLENGANSSFVNQIVDEAVPLDRLVGDPIETVRAQGGLPHPAIAVPHRLYGEERK 540 YLVRRLLENGANSSFVNQIVDEAVPLDRLVGDPIETVRAQGGLPHPAIAVPHRLYGEERK Sbjct: 481 YLVRRLLENGANSSFVNQIVDEAVPLDRLVGDPIETVRAQGGLPHPAIAVPHRLYGEERK 540 Query: 541 NSAGIDLSNEDRLQQLGQLFISMADRQWQAAPLLAADTAAQSAQAAQLVRNPADLREVVG 600 NSAGIDLSNEDRLQQLGQLFISMADRQWQAAPLLAADTAAQSAQAAQLVRNPADLREVVG Sbjct: 541 NSAGIDLSNEDRLQQLGQLFISMADRQWQAAPLLAADTAAQSAQAAQLVRNPADLREVVG 600 Query: 601 QVSEATVADVDTALRAATDYAPQWQSTPATERAAMLERAADLLEEHIAELMALAVREAGK 660 QVSEATVADVDTALRAATDYAPQWQSTPATERAAMLERAADLLEEHIAELMALAVREAGK Sbjct: 601 QVSEATVADVDTALRAATDYAPQWQSTPATERAAMLERAADLLEEHIAELMALAVREAGK 660 Query: 661 SLPNAIAEVREAVDFLRYYAIASRHDGNVLAWGPVVCISPWNFPLAIFIGEVSAALAAGN 720 SLPNAIAEVREAVDFLRYYAIASRHDGNVLAWGPVVCISPWNFPLAIFIGEVSAALAAGN Sbjct: 661 SLPNAIAEVREAVDFLRYYAIASRHDGNVLAWGPVVCISPWNFPLAIFIGEVSAALAAGN 720 Query: 721 VVLAKPAEQTALIAHRAVQLLHEAGIPRAALQLLPGRGETVGAALTSDVRVKGVIFTGST 780 VVLAKPAEQTALIAHRAVQLLHEAGIPRAALQLLPGRGETVGAALTSDVRVKGVIFTGST Sbjct: 721 VVLAKPAEQTALIAHRAVQLLHEAGIPRAALQLLPGRGETVGAALTSDVRVKGVIFTGST 780 Query: 781 EVAQLINRTLAQRQHDDGDGSGEHGEVPLIAETGGQNALIVDSSALAEQVVQDVLSSAFD 840 EVAQLINRTLAQRQHDDGDGSGEHGEVPLIAETGGQNALIVDSSALAEQVVQDVLSSAFD Sbjct: 781 EVAQLINRTLAQRQHDDGDGSGEHGEVPLIAETGGQNALIVDSSALAEQVVQDVLSSAFD 840 Query: 841 SAGQRCSALRILCLQEDIADRTLAMLKGAMAELRVGRPDRLSIDIGPVIDAEARQNLLDH 900 SAGQRCSALRILCLQEDIADRTLAMLKGAMAELRVGRPDRLSIDIGPVIDAEARQNLLDH Sbjct: 841 SAGQRCSALRILCLQEDIADRTLAMLKGAMAELRVGRPDRLSIDIGPVIDAEARQNLLDH 900 Query: 901 IERMRASARAVHQLPLGEECQHGTFVAPTVIEIDDLAQLQREVFGPVLHVLRYRRDALPQ 960 IERMRASARAVHQLPLGEECQHGTFVAPTVIEIDDLAQLQREVFGPVLHVLRYRRDALPQ Sbjct: 901 IERMRASARAVHQLPLGEECQHGTFVAPTVIEIDDLAQLQREVFGPVLHVLRYRRDALPQ 960 Query: 961 LIDAINATGYGLTLGVHSRIDETIEFVAQRAHVGNIYVNRNIVGAVVGVQPFGGEGKSGT 1020 LIDAINATGYGLTLGVHSRIDETIEFVAQRAHVGNIYVNRNIVGAVVGVQPFGGEGKSGT Sbjct: 961 LIDAINATGYGLTLGVHSRIDETIEFVAQRAHVGNIYVNRNIVGAVVGVQPFGGEGKSGT 1020 Query: 1021 GPKAGGPLYLKRLQRNAQLHEELTRAQPADVPNALLDSLLDWARTHGHERLAANGQRYHR 1080 GPKAGGPLYLKRLQRNAQLHEELTRAQPADVPNALLDSLLDWARTHGHERLAANGQRYHR Sbjct: 1021 GPKAGGPLYLKRLQRNAQLHEELTRAQPADVPNALLDSLLDWARTHGHERLAANGQRYHR 1080 Query: 1081 DSLLQRSLVLPGPTGERNTLGFAPRGLVLCAAGSVGTLLNQLAAAFATGNTALVDERSAA 1140 DSLLQRSLVLPGPTGERNTLGFAPRGLVLCAAGSVGTLLNQLAAAFATGNTALVDERSAA Sbjct: 1081 DSLLQRSLVLPGPTGERNTLGFAPRGLVLCAAGSVGTLLNQLAAAFATGNTALVDERSAA 1140 Query: 1141 ILPSGLPAPVRAAIRRASQLDAEPLQAALVDSHQAAHWRARLAAREGALVPLILCGEDTT 1200 ILPSGLPAPVRAAIRRASQLDAEPLQAALVDSHQAAHWRARLAAREGALVPLILCGEDTT Sbjct: 1141 ILPSGLPAPVRAAIRRASQLDAEPLQAALVDSHQAAHWRARLAAREGALVPLILCGEDTT 1200 Query: 1201 IPLWRLLAERALCINTTAAGGNASLMTISV 1230 IPLWRLLAERALCINTTAAGGNASLMTISV Sbjct: 1201 IPLWRLLAERALCINTTAAGGNASLMTISV 1230 Lambda K H 0.319 0.134 0.389 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: 4244 Number of extensions: 128 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: 1230 Length of database: 1230 Length adjustment: 47 Effective length of query: 1183 Effective length of database: 1183 Effective search space: 1399489 Effective search space used: 1399489 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