Alignments for a candidate for glcB in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for glcB in Shewanella oneidensis MR-1

Align Malate synthase (EC 2.3.3.9) (characterized)
to candidate 200654 SO1483 malate synthase A (NCBI ptt file)

Query= reanno::MR1:200654
         (549 letters)



>FitnessBrowser__MR1:200654
          Length = 549

 Score = 1109 bits (2868), Expect = 0.0
 Identities = 549/549 (100%), Positives = 549/549 (100%)

Query: 1   MTEHTLSEQQVNLTLNKATANGTLALVGNTIPGQEVIFTEGAMALLESLCREFGAEVPTL 60
           MTEHTLSEQQVNLTLNKATANGTLALVGNTIPGQEVIFTEGAMALLESLCREFGAEVPTL
Sbjct: 1   MTEHTLSEQQVNLTLNKATANGTLALVGNTIPGQEVIFTEGAMALLESLCREFGAEVPTL 60

Query: 61  LAKRKDRQARIDKGALPDFLPETRAIRDGAWKIRGIPNDLLDRRVEITGPVERKMVINAL 120
           LAKRKDRQARIDKGALPDFLPETRAIRDGAWKIRGIPNDLLDRRVEITGPVERKMVINAL
Sbjct: 61  LAKRKDRQARIDKGALPDFLPETRAIRDGAWKIRGIPNDLLDRRVEITGPVERKMVINAL 120

Query: 121 NANAKVFMADFEDSLAPSWQKVVEGQINLRDAVRGEIEYTAPETGKHYKLGPNPAVLICR 180
           NANAKVFMADFEDSLAPSWQKVVEGQINLRDAVRGEIEYTAPETGKHYKLGPNPAVLICR
Sbjct: 121 NANAKVFMADFEDSLAPSWQKVVEGQINLRDAVRGEIEYTAPETGKHYKLGPNPAVLICR 180

Query: 181 VRGLHLKEKHVEFNQQSIPGGLFDFAMYFYHNYRQLLAKGSGPYFYIPKLESHIEARWWA 240
           VRGLHLKEKHVEFNQQSIPGGLFDFAMYFYHNYRQLLAKGSGPYFYIPKLESHIEARWWA
Sbjct: 181 VRGLHLKEKHVEFNQQSIPGGLFDFAMYFYHNYRQLLAKGSGPYFYIPKLESHIEARWWA 240

Query: 241 KVFAFVEERFCLQAGTIKCTCLIETLPAVFEMDEILYELRSNIVALNCGRWDYIFSYIKT 300
           KVFAFVEERFCLQAGTIKCTCLIETLPAVFEMDEILYELRSNIVALNCGRWDYIFSYIKT
Sbjct: 241 KVFAFVEERFCLQAGTIKCTCLIETLPAVFEMDEILYELRSNIVALNCGRWDYIFSYIKT 300

Query: 301 LKRHGDRVLPDRQAVTMDTPFLSAYSRLLIKTCHKRGALAMGGMAAFIPAKDPAQNEAVL 360
           LKRHGDRVLPDRQAVTMDTPFLSAYSRLLIKTCHKRGALAMGGMAAFIPAKDPAQNEAVL
Sbjct: 301 LKRHGDRVLPDRQAVTMDTPFLSAYSRLLIKTCHKRGALAMGGMAAFIPAKDPAQNEAVL 360

Query: 361 QRVRKDKELEARNGHDGTWVAHPGLADTAMGIFNEYIGQDHQNQLHITRDVDAPILAAEL 420
           QRVRKDKELEARNGHDGTWVAHPGLADTAMGIFNEYIGQDHQNQLHITRDVDAPILAAEL
Sbjct: 361 QRVRKDKELEARNGHDGTWVAHPGLADTAMGIFNEYIGQDHQNQLHITRDVDAPILAAEL 420

Query: 421 LKTCDGERTEQGMRLNIRIALQYLEAWISGNGCVPIYGLMEDAATAEISRASIWQWIQHG 480
           LKTCDGERTEQGMRLNIRIALQYLEAWISGNGCVPIYGLMEDAATAEISRASIWQWIQHG
Sbjct: 421 LKTCDGERTEQGMRLNIRIALQYLEAWISGNGCVPIYGLMEDAATAEISRASIWQWIQHG 480

Query: 481 KSLSNGKLVTKQLFKDMLVEELANVKKEVGSDRFTHGKFTQAAVLLEDITTSDELVDFLT 540
           KSLSNGKLVTKQLFKDMLVEELANVKKEVGSDRFTHGKFTQAAVLLEDITTSDELVDFLT
Sbjct: 481 KSLSNGKLVTKQLFKDMLVEELANVKKEVGSDRFTHGKFTQAAVLLEDITTSDELVDFLT 540

Query: 541 LPGYEMLTA 549
           LPGYEMLTA
Sbjct: 541 LPGYEMLTA 549


Lambda     K      H
   0.321    0.137    0.411 

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: 1087
Number of extensions: 15
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: 549
Length of database: 549
Length adjustment: 36
Effective length of query: 513
Effective length of database: 513
Effective search space:   263169
Effective search space used:   263169
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: 53 (25.0 bits)

Align candidate 200654 SO1483 (malate synthase A (NCBI ptt file))
to HMM TIGR01344 (aceB: malate synthase A (EC 2.3.3.9))

# 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/TIGR01344.hmm
# target sequence database:        /tmp/gapView.24559.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01344  [M=511]
Accession:   TIGR01344
Description: malate_syn_A: malate synthase A
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   4.4e-250  816.1   0.0   5.1e-250  815.9   0.0    1.0  1  lcl|FitnessBrowser__MR1:200654  SO1483 malate synthase A (NCBI p


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:200654  SO1483 malate synthase A (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  815.9   0.0  5.1e-250  5.1e-250       1     510 [.      37     547 ..      37     548 .. 0.99

  Alignments for each domain:
  == domain 1  score: 815.9 bits;  conditional E-value: 5.1e-250
                       TIGR01344   1 vltkealeflaelhrrfaerrkellarrekkqakldkgelldflpetkeireddwkvaaipadlldrrveitGPvdrkm 79 
                                     ++t+ a+++l +l+r+f + +  lla+r+++qa++dkg+l+dflpet++ir++ wk+  ip+dlldrrveitGPv+rkm
  lcl|FitnessBrowser__MR1:200654  37 IFTEGAMALLESLCREFGAEVPTLLAKRKDRQARIDKGALPDFLPETRAIRDGAWKIRGIPNDLLDRRVEITGPVERKM 115
                                     799**************************************************************************** PP

                       TIGR01344  80 vinalnaeakvfladfedsssPtwenvveGqinlkdairgeidftdeesgkeyalkaklavlivrprGwhlkerhleid 158
                                     vinalna+akvf+adfeds +P+w++vveGqinl+da+rgei++t++e+gk+y+l ++ avli+r+rG+hlke+h+e +
  lcl|FitnessBrowser__MR1:200654 116 VINALNANAKVFMADFEDSLAPSWQKVVEGQINLRDAVRGEIEYTAPETGKHYKLGPNPAVLICRVRGLHLKEKHVEFN 194
                                     ******************************************************************************* PP

                       TIGR01344 159 gkaisgslldfglyffhnarellkkGkGPyfylPkleshlearlwndvfllaqevlglprGtikatvlietlpaafemd 237
                                     +++i+g l+df++yf+hn r+ll+kG+GPyfy+Pklesh+ear+w  vf + +e + l+ Gtik t lietlpa+femd
  lcl|FitnessBrowser__MR1:200654 195 QQSIPGGLFDFAMYFYHNYRQLLAKGSGPYFYIPKLESHIEARWWAKVFAFVEERFCLQAGTIKCTCLIETLPAVFEMD 273
                                     ******************************************************************************* PP

                       TIGR01344 238 eilyelrehssGlncGrwdyifslikklkkaeevvlPdrdavtmdkaflnaysklliqtchrrgafalGGmaafiPikd 316
                                     eilyelr  ++ lncGrwdyifs+ik+lk++ ++vlPdr+avtmd++fl+ays+lli+tch+rga a+GGmaafiP+k 
  lcl|FitnessBrowser__MR1:200654 274 EILYELRSNIVALNCGRWDYIFSYIKTLKRHGDRVLPDRQAVTMDTPFLSAYSRLLIKTCHKRGALAMGGMAAFIPAK- 351
                                     ******************************************************************************. PP

                       TIGR01344 317 dpaaneaalekvradkereaknGhdGtwvahPdlvevalevfdevlge..pnqldrvrledvsitaaellevkdasrte 393
                                     dpa nea+l++vr dke+ea+nGhdGtwvahP+l+++a+ +f+e++g+  +nql+ +r++d++i aaell+++d++rte
  lcl|FitnessBrowser__MR1:200654 352 DPAQNEAVLQRVRKDKELEARNGHDGTWVAHPGLADTAMGIFNEYIGQdhQNQLHITRDVDAPILAAELLKTCDGERTE 430
                                     **********************************************987789999************************ PP

                       TIGR01344 394 eGlrenirvglryieawlrGsGavpiynlmedaataeisraqlwqwikhGvvledGekvtselvrdllkeeleklkkes 472
                                     +G+r nir++l+y+eaw++G+G+vpiy lmedaataeisra++wqwi+hG++l++G+ vt++l++d+l eel+++kke+
  lcl|FitnessBrowser__MR1:200654 431 QGMRLNIRIALQYLEAWISGNGCVPIYGLMEDAATAEISRASIWQWIQHGKSLSNGKLVTKQLFKDMLVEELANVKKEV 509
                                     ******************************************************************************* PP

                       TIGR01344 473 gkeeyakarleeaaellerlvlseeledfltlpaydel 510
                                     g+++++++++++aa lle +++s+el dfltlp+y++l
  lcl|FitnessBrowser__MR1:200654 510 GSDRFTHGKFTQAAVLLEDITTSDELVDFLTLPGYEML 547
                                     ************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (511 nodes)
Target sequences:                          1  (549 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 12.77
//
[ok]

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:

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