GapMind for catabolism of small carbon sources

 

Alignments for a candidate for put1 in Herbaspirillum seropedicae SmR1

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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