GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__HerbieS:HSERO_RS00905 HSERO_RS00905 bifunctional
            proline dehydrogenase/pyrroline-5-carboxylate
            dehydrogenase
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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