Alignments for a candidate for glcB in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for glcB in Shewanella amazonensis SB2B

Align Malate synthase (EC 2.3.3.9) (characterized)
to candidate 6938261 Sama_2381 malate synthase (RefSeq)

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



>FitnessBrowser__SB2B:6938261
          Length = 543

 Score =  911 bits (2354), Expect = 0.0
 Identities = 449/548 (81%), Positives = 481/548 (87%), Gaps = 9/548 (1%)

Query: 1   MTEHTLSEQQVNLTLNKATANGTLALVGNTIPGQEVIFTEGAMALLESLCREFGAEVPTL 60
           MTE  + + Q        T  G L L G+ I GQE +FTEGAM+LLESLC  F  +V  L
Sbjct: 1   MTEQMMEQPQ--------TLTG-LKLAGHHIQGQEEVFTEGAMSLLESLCARFAGDVDAL 51

Query: 61  LAKRKDRQARIDKGALPDFLPETRAIRDGAWKIRGIPNDLLDRRVEITGPVERKMVINAL 120
           LAKRK+RQ RIDKG LPDFLPETRAIRDG W IRGIP DL DRRVEITGPV+RKM+INAL
Sbjct: 52  LAKRKERQVRIDKGELPDFLPETRAIRDGKWTIRGIPTDLQDRRVEITGPVDRKMIINAL 111

Query: 121 NANAKVFMADFEDSLAPSWQKVVEGQINLRDAVRGEIEYTAPETGKHYKLGPNPAVLICR 180
           NA+ KVFMADFEDSLAPSW+KV++GQINLRDAVRG IEY AP+TGK Y+L  NPAVLI R
Sbjct: 112 NADVKVFMADFEDSLAPSWEKVIQGQINLRDAVRGTIEYKAPDTGKEYRLNDNPAVLIAR 171

Query: 181 VRGLHLKEKHVEFNQQSIPGGLFDFAMYFYHNYRQLLAKGSGPYFYIPKLESHIEARWWA 240
           VRGLHLKEKHVEFN QSIPG LFDF  YFYHNYRQLL+KGSGPYFYIPKLESH+EARWWA
Sbjct: 172 VRGLHLKEKHVEFNGQSIPGALFDFCFYFYHNYRQLLSKGSGPYFYIPKLESHLEARWWA 231

Query: 241 KVFAFVEERFCLQAGTIKCTCLIETLPAVFEMDEILYELRSNIVALNCGRWDYIFSYIKT 300
           KVFAF EERFCL+ GTIKCTCLIETLPAVFEMDEILYELRSNIVALNCGRWDYIFSYIKT
Sbjct: 232 KVFAFTEERFCLEPGTIKCTCLIETLPAVFEMDEILYELRSNIVALNCGRWDYIFSYIKT 291

Query: 301 LKRHGDRVLPDRQAVTMDTPFLSAYSRLLIKTCHKRGALAMGGMAAFIPAKDPAQNEAVL 360
           LK H DRVLPDRQ VTMD PFLSAYSRLLIKTCHKRGALAMGGMAAFIPAKD   N  VL
Sbjct: 292 LKHHSDRVLPDRQQVTMDKPFLSAYSRLLIKTCHKRGALAMGGMAAFIPAKDAEANRLVL 351

Query: 361 QRVRKDKELEARNGHDGTWVAHPGLADTAMGIFNEYIGQDHQNQLHITRDVDAPILAAEL 420
           +RV KDKELEARNGHDGTWVAHPGLA TAM +FN++IG DH NQLHITRDVDAPILA+EL
Sbjct: 352 ERVCKDKELEARNGHDGTWVAHPGLAQTAMAVFNQFIGDDHCNQLHITRDVDAPILASEL 411

Query: 421 LKTCDGERTEQGMRLNIRIALQYLEAWISGNGCVPIYGLMEDAATAEISRASIWQWIQHG 480
           L  C+GERTE GMRLNIRIALQY+EAWISGNGCVPIYGLMEDAATAEISRASIWQWI H 
Sbjct: 412 LAPCEGERTEHGMRLNIRIALQYIEAWISGNGCVPIYGLMEDAATAEISRASIWQWIHHQ 471

Query: 481 KSLSNGKLVTKQLFKDMLVEELANVKKEVGSDRFTHGKFTQAAVLLEDITTSDELVDFLT 540
           K LSNGKLVTK L K+MLVEELANVK+EVGS+RFTHG+FTQAAVLLE+ITT+DELVDFLT
Sbjct: 472 KHLSNGKLVTKALLKEMLVEELANVKEEVGSERFTHGRFTQAAVLLEEITTADELVDFLT 531

Query: 541 LPGYEMLT 548
           LPGYE+LT
Sbjct: 532 LPGYELLT 539


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: 1004
Number of extensions: 22
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: 543
Length adjustment: 35
Effective length of query: 514
Effective length of database: 508
Effective search space:   261112
Effective search space used:   261112
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: 52 (24.6 bits)

Align candidate 6938261 Sama_2381 (malate synthase (RefSeq))
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.3459.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.1e-246  804.9   0.0   1.3e-246  804.7   0.0    1.0  1  lcl|FitnessBrowser__SB2B:6938261  Sama_2381 malate synthase (RefSe


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6938261  Sama_2381 malate synthase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  804.7   0.0  1.3e-246  1.3e-246       1     510 [.      28     538 ..      28     539 .. 0.99

  Alignments for each domain:
  == domain 1  score: 804.7 bits;  conditional E-value: 1.3e-246
                         TIGR01344   1 vltkealeflaelhrrfaerrkellarrekkqakldkgelldflpetkeireddwkvaaipadlldrrveitGPvdr 77 
                                       v+t+ a+++l +l+ rfa  +++lla+r+++q ++dkgel+dflpet++ir+++w++  ip+dl+drrveitGPvdr
  lcl|FitnessBrowser__SB2B:6938261  28 VFTEGAMSLLESLCARFAGDVDALLAKRKERQVRIDKGELPDFLPETRAIRDGKWTIRGIPTDLQDRRVEITGPVDR 104
                                       799************************************************************************** PP

                         TIGR01344  78 kmvinalnaeakvfladfedsssPtwenvveGqinlkdairgeidftdeesgkeyalkaklavlivrprGwhlkerh 154
                                       km+inalna++kvf+adfeds +P+we+v++Gqinl+da+rg+i+++++++gkey+l+ + avli r+rG+hlke+h
  lcl|FitnessBrowser__SB2B:6938261 105 KMIINALNADVKVFMADFEDSLAPSWEKVIQGQINLRDAVRGTIEYKAPDTGKEYRLNDNPAVLIARVRGLHLKEKH 181
                                       ***************************************************************************** PP

                         TIGR01344 155 leidgkaisgslldfglyffhnarellkkGkGPyfylPkleshlearlwndvfllaqevlglprGtikatvlietlp 231
                                       +e +g++i+g+l+df +yf+hn r+ll+kG+GPyfy+Pkleshlear+w  vf +++e + l+ Gtik t lietlp
  lcl|FitnessBrowser__SB2B:6938261 182 VEFNGQSIPGALFDFCFYFYHNYRQLLSKGSGPYFYIPKLESHLEARWWAKVFAFTEERFCLEPGTIKCTCLIETLP 258
                                       ***************************************************************************** PP

                         TIGR01344 232 aafemdeilyelrehssGlncGrwdyifslikklkkaeevvlPdrdavtmdkaflnaysklliqtchrrgafalGGm 308
                                       a+femdeilyelr  ++ lncGrwdyifs+ik+lk+++++vlPdr++vtmdk+fl+ays+lli+tch+rga a+GGm
  lcl|FitnessBrowser__SB2B:6938261 259 AVFEMDEILYELRSNIVALNCGRWDYIFSYIKTLKHHSDRVLPDRQQVTMDKPFLSAYSRLLIKTCHKRGALAMGGM 335
                                       ***************************************************************************** PP

                         TIGR01344 309 aafiPikddpaaneaalekvradkereaknGhdGtwvahPdlvevalevfdevlge..pnqldrvrledvsitaael 383
                                       aafiP+k d++an+ +le+v  dke+ea+nGhdGtwvahP+l+++a++vf++++g+   nql+ +r++d++i a+el
  lcl|FitnessBrowser__SB2B:6938261 336 AAFIPAK-DAEANRLVLERVCKDKELEARNGHDGTWVAHPGLAQTAMAVFNQFIGDdhCNQLHITRDVDAPILASEL 411
                                       *******.***********************************************97789***************** PP

                         TIGR01344 384 levkdasrteeGlrenirvglryieawlrGsGavpiynlmedaataeisraqlwqwikhGvvledGekvtselvrdl 460
                                       l+ ++++rte+G+r nir++l+yieaw++G+G+vpiy lmedaataeisra++wqwi+h + l++G+ vt++l++++
  lcl|FitnessBrowser__SB2B:6938261 412 LAPCEGERTEHGMRLNIRIALQYIEAWISGNGCVPIYGLMEDAATAEISRASIWQWIHHQKHLSNGKLVTKALLKEM 488
                                       ***************************************************************************** PP

                         TIGR01344 461 lkeeleklkkesgkeeyakarleeaaellerlvlseeledfltlpaydel 510
                                       l eel+++k+e+g+e+++++r+++aa lle++++++el dfltlp+y+ l
  lcl|FitnessBrowser__SB2B:6938261 489 LVEELANVKEEVGSERFTHGRFTQAAVLLEEITTADELVDFLTLPGYELL 538
                                       ************************************************88 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (511 nodes)
Target sequences:                          1  (543 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 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 8.15
//
[ok]

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

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Protein sequences (fasta format)
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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