Alignments for a candidate for rocA in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for rocA 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)

Align candidate HSERO_RS00905 HSERO_RS00905 (bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase)
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.3673.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   1.1e-239  781.9   4.6     2e-239  781.1   4.6    1.4  1  lcl|FitnessBrowser__HerbieS:HSERO_RS00905  HSERO_RS00905 bifunctional proli


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS00905  HSERO_RS00905 bifunctional proline dehydrogenase/pyrroline-5-carboxylate d
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  781.1   4.6    2e-239    2e-239       2     497 ..     534    1035 ..     533    1038 .. 0.97

  Alignments for each domain:
  == domain 1  score: 781.1 bits;  conditional E-value: 2e-239
                                  TIGR01238    2 lygegrknslGvdlaneselksleeqllkaaakkfqaapivgeka..kaegeaqpvknpadrkdiv 65  
                                                 lyge rkns+G+dl+ne++l++l + + ++a++++qaap+++ ++  ++ + aq v+npad +++v
  lcl|FitnessBrowser__HerbieS:HSERO_RS00905  534 LYGEERKNSAGIDLSNEDRLQQLGQLFISMADRQWQAAPLLAADTaaQSAQAAQLVRNPADLREVV 599 
                                                 8****************************************944423677889************* PP

                                  TIGR01238   66 GqvseadaaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsna 131 
                                                 Gqvsea  a+v+ a+ +a + +++w++t+a eraa+ler+adlle+h+ el+al+vreaGk+l na
  lcl|FitnessBrowser__HerbieS:HSERO_RS00905  600 GQVSEATVADVDTALRAATDYAPQWQSTPATERAAMLERAADLLEEHIAELMALAVREAGKSLPNA 665 
                                                 ****************************************************************** PP

                                  TIGR01238  132 iaevreavdflryyakqvedvldeesakalGavvcispwnfplaiftGqiaaalaaGntviakpae 197 
                                                 iaevreavdflryya   +++    ++ a G+vvcispwnfplaif+G+++aalaaGn v+akpae
  lcl|FitnessBrowser__HerbieS:HSERO_RS00905  666 IAEVREAVDFLRYYAIASRHDG---NVLAWGPVVCISPWNFPLAIFIGEVSAALAAGNVVLAKPAE 728 
                                                 ***************9998764...3679************************************* PP

                                  TIGR01238  198 qtsliaaravellqeaGvpagviqllpGrGedvGaaltsderiaGviftGstevarlinkalakre 263 
                                                 qt+lia rav+ll+eaG+p +++qllpGrGe+vGaaltsd r++GviftGsteva+lin++la+r+
  lcl|FitnessBrowser__HerbieS:HSERO_RS00905  729 QTALIAHRAVQLLHEAGIPRAALQLLPGRGETVGAALTSDVRVKGVIFTGSTEVAQLINRTLAQRQ 794 
                                                 *****************************************************************9 PP

                                  TIGR01238  264 dap.........vpliaetGGqnamivdstalaeqvvadvlasafdsaGqrcsalrvlcvqedvad 320 
                                                  ++         vpliaetGGqna+ivds+alaeqvv+dvl+safdsaGqrcsalr+lc+qed+ad
  lcl|FitnessBrowser__HerbieS:HSERO_RS00905  795 HDDgdgsgehgeVPLIAETGGQNALIVDSSALAEQVVQDVLSSAFDSAGQRCSALRILCLQEDIAD 860 
                                                 887788999999****************************************************** PP

                                  TIGR01238  321 rvltlikGamdelkvgkpirlttdvGpvidaeakqnllahiekmkakakkvaqvkleddvesekgt 386 
                                                 r+l ++kGam el+vg+p rl  d+Gpvidaea+qnll hie+m+a a+ v+q+ l +  e+++gt
  lcl|FitnessBrowser__HerbieS:HSERO_RS00905  861 RTLAMLKGAMAELRVGRPDRLSIDIGPVIDAEARQNLLDHIERMRASARAVHQLPLGE--ECQHGT 924 
                                                 ********************************************************99..****** PP

                                  TIGR01238  387 fvaptlfelddldelkkevfGpvlhvvrykadeldkvvdkinakGygltlGvhsrieetvrqiekr 452 
                                                 fvapt++e+ddl++l++evfGpvlhv+ry++d l +++d ina+GygltlGvhsri+et+ ++ +r
  lcl|FitnessBrowser__HerbieS:HSERO_RS00905  925 FVAPTVIEIDDLAQLQREVFGPVLHVLRYRRDALPQLIDAINATGYGLTLGVHSRIDETIEFVAQR 990 
                                                 ****************************************************************** PP

                                  TIGR01238  453 akvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrltr 497 
                                                 a+vGn+yvnrn+vGavvGvqpfGGeG sGtGpkaGGplyl+rl r
  lcl|FitnessBrowser__HerbieS:HSERO_RS00905  991 AHVGNIYVNRNIVGAVVGVQPFGGEGKSGTGPKAGGPLYLKRLQR 1035
                                                 ******************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (500 nodes)
Target sequences:                          1  (1230 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 22.37
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources