Alignments for a candidate for glcB in Flavobacterium sp. LM5

GapMind for catabolism of small carbon sources

Alignments for a candidate for glcB in Flavobacterium sp. LM5

Align malate synthase (EC 2.3.3.9) (characterized)
to candidate WP_078210938.1 BXU11_RS02770 malate synthase A

Query= BRENDA::Q5YLB8
         (539 letters)



>NCBI__GCF_002017945.1:WP_078210938.1
          Length = 533

 Score =  548 bits (1411), Expect = e-160
 Identities = 274/504 (54%), Positives = 353/504 (70%), Gaps = 6/504 (1%)

Query: 24  ILTKEATAFLALLHRTFNPTRKALLQRRSDRQAELDRGSLLDFLPETKHIRDNDAWKGAP 83
           ILT+EA  FL  LH  FN  R  LL+ R  +Q + D G L  F  ETK IR+++ W+ AP
Sbjct: 25  ILTEEAIDFLTALHENFNTKRLELLEARKAQQVQFDNGVLPTFPLETKSIRESN-WQAAP 83

Query: 84  PAPGLVDRRVEITGPTDRKMVVNALNSDVYTYMADFEDSSAPTWDNMVNGQVNLYDAIRR 143
               L+DRRVEITGP DRKMV+NALNS   T+MADFEDS++PTWDN++ GQ NL DA+ +
Sbjct: 84  VPKDLIDRRVEITGPVDRKMVINALNSGAKTFMADFEDSTSPTWDNIMEGQQNLKDAVNK 143

Query: 144 QVDFKQGGKDYKLRTDRKLPTLIARARGWHLDEKHLTVDGEPMSGSLFDFGLYFFHNAKE 203
            +  +   K+ K     K   LI R RG HL+EKH+ +  E  SGSL DFGLY FHN  +
Sbjct: 144 TITLEDPIKNKKYALKDKTAVLIVRPRGLHLNEKHILIANEEASGSLIDFGLYAFHNHDQ 203

Query: 204 LVKRGAGPYFYLPKMESHLEARMWNDVYNLAQDYIGMPRGTIRATVLIETISAAFEMDEI 263
           L + G+ PYFYLPK+E +LEAR WN+V+  AQ+Y+G   GT +ATVLIETI+A+F++DEI
Sbjct: 204 LARNGSAPYFYLPKLEHYLEARWWNEVFEFAQEYLGEQHGTFKATVLIETITASFQLDEI 263

Query: 264 IYELRDHSSGLNCGRWDYIFSFIKKFRQNPSFVLPDRSDVTMTVPFMDAYVKLLIKTCHR 323
           IYELRDH  GLNCGRWDYIFS+IKKFR NP+F++P+R  VTMT PFMDAY KL+I+ CH+
Sbjct: 264 IYELRDHIVGLNCGRWDYIFSYIKKFRNNPAFIVPNRDQVTMTSPFMDAYSKLVIQRCHK 323

Query: 324 RGVHAMGGMAAQIPIKDDPKANEAAMASVRADKLREVRAGHDGTWVGHPALAKIATDVFD 383
           R +HAMGGMAAQIPIK+DP+ANE A   V ADK RE R GHDGTWV HP L  IA  VF+
Sbjct: 324 RNIHAMGGMAAQIPIKNDPEANEIAFKKVIADKEREARNGHDGTWVAHPDLVPIAMKVFN 383

Query: 384 QYMPTPNQLFVRREDVHITANDLLNTNVPGRITEDGIRKNLNIGLSYMEGWLRGVGCIPI 443
           + M T N + ++R D+HIT  DLL   V G ITE+GIRKN+N+ + Y+  WL G G   I
Sbjct: 384 ENMMTKNHIHIKRADLHITEADLLQIPV-GTITEEGIRKNVNVAVLYITSWLNGQGAAAI 442

Query: 444 NYLMEDAATAEVSRSQLWQWVKHNVTTAEGKRV-DKAY---ALKLLQEQTDELASKAPKG 499
           ++LMEDAATAE+SRSQLWQW+++ VT   G+++  K Y   AL+  ++   ++  +A + 
Sbjct: 443 HHLMEDAATAEISRSQLWQWLQNEVTLDSGEKLTTKLYHRIALEEYEKIRKQVGDRAHEE 502

Query: 500 NRYQLAARYFAGQVAGEDYADFLT 523
             Y LA +     V  + + +FLT
Sbjct: 503 ENYILAEKLLDELVVNKKFVEFLT 526


Lambda     K      H
   0.320    0.136    0.410 

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: 741
Number of extensions: 31
Number of successful extensions: 3
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: 539
Length of database: 533
Length adjustment: 35
Effective length of query: 504
Effective length of database: 498
Effective search space:   250992
Effective search space used:   250992
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 WP_078210938.1 BXU11_RS02770 (malate synthase A)
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.3081382.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     6e-236  769.5   2.7   6.8e-236  769.3   2.7    1.0  1  NCBI__GCF_002017945.1:WP_078210938.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002017945.1:WP_078210938.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  769.3   2.7  6.8e-236  6.8e-236       1     510 [.      25     533 .]      25     533 .] 1.00

  Alignments for each domain:
  == domain 1  score: 769.3 bits;  conditional E-value: 6.8e-236
                             TIGR01344   1 vltkealeflaelhrrfaerrkellarrekkqakldkgelldflpetkeireddwkvaaipadlldrrveitG 73 
                                           +lt+ea+ fl+ lh++f+++r ell++r+++q ++d+g l+ f  etk+ire++w+ a++p+dl+drrveitG
  NCBI__GCF_002017945.1:WP_078210938.1  25 ILTEEAIDFLTALHENFNTKRLELLEARKAQQVQFDNGVLPTFPLETKSIRESNWQAAPVPKDLIDRRVEITG 97 
                                           89*********************************************************************** PP

                             TIGR01344  74 PvdrkmvinalnaeakvfladfedsssPtwenvveGqinlkdairgeidftdeesgkeyalkaklavlivrpr 146
                                           Pvdrkmvinaln++ak+f+adfeds+sPtw+n++eGq nlkda++++i+  d+ ++k+yalk k+avlivrpr
  NCBI__GCF_002017945.1:WP_078210938.1  98 PVDRKMVINALNSGAKTFMADFEDSTSPTWDNIMEGQQNLKDAVNKTITLEDPIKNKKYALKDKTAVLIVRPR 170
                                           ************************************************************************* PP

                             TIGR01344 147 GwhlkerhleidgkaisgslldfglyffhnarellkkGkGPyfylPkleshlearlwndvfllaqevlglprG 219
                                           G+hl+e+h+ i ++  sgsl+dfgly+fhn+ +l ++G+ PyfylPkle++lear+wn+vf +aqe+lg ++G
  NCBI__GCF_002017945.1:WP_078210938.1 171 GLHLNEKHILIANEEASGSLIDFGLYAFHNHDQLARNGSAPYFYLPKLEHYLEARWWNEVFEFAQEYLGEQHG 243
                                           ************************************************************************* PP

                             TIGR01344 220 tikatvlietlpaafemdeilyelrehssGlncGrwdyifslikklkkaeevvlPdrdavtmdkaflnayskl 292
                                           t katvliet++a+f++dei+yelr+h++GlncGrwdyifs+ikk+++++++++P+rd+vtm+++f++ayskl
  NCBI__GCF_002017945.1:WP_078210938.1 244 TFKATVLIETITASFQLDEIIYELRDHIVGLNCGRWDYIFSYIKKFRNNPAFIVPNRDQVTMTSPFMDAYSKL 316
                                           ************************************************************************* PP

                             TIGR01344 293 liqtchrrgafalGGmaafiPikddpaaneaalekvradkereaknGhdGtwvahPdlvevalevfdevlgep 365
                                           +iq ch+r+++a+GGmaa+iPik+dp+ane a++kv adkerea+nGhdGtwvahPdlv++a++vf+e + ++
  NCBI__GCF_002017945.1:WP_078210938.1 317 VIQRCHKRNIHAMGGMAAQIPIKNDPEANEIAFKKVIADKEREARNGHDGTWVAHPDLVPIAMKVFNENMMTK 389
                                           ************************************************************************* PP

                             TIGR01344 366 nqldrvrledvsitaaellevkdasrteeGlrenirvglryieawlrGsGavpiynlmedaataeisraqlwq 438
                                           n ++ +r +d++it+a+ll+++ ++ teeG+r+n++v++ yi +wl+G+Ga +i++lmedaataeisr+qlwq
  NCBI__GCF_002017945.1:WP_078210938.1 390 NHIHIKR-ADLHITEADLLQIPVGTITEEGIRKNVNVAVLYITSWLNGQGAAAIHHLMEDAATAEISRSQLWQ 461
                                           *****88.***************************************************************** PP

                             TIGR01344 439 wikhGvvledGekvtselvrdllkeeleklkkesgkeeyakarleeaaellerlvlseeledfltlpaydel 510
                                           w+++ v+l+ Gek+t++l   ++ ee ek++k++g+  + ++++  a++ll +lv+++++ +flt+p+y++l
  NCBI__GCF_002017945.1:WP_078210938.1 462 WLQNEVTLDSGEKLTTKLYHRIALEEYEKIRKQVGDRAHEEENYILAEKLLDELVVNKKFVEFLTIPGYKYL 533
                                           *********************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (511 nodes)
Target sequences:                          1  (533 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: 00:00:00.01
# Mc/sec: 21.89
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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 2024 update 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