Alignments for a candidate for glcB in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for glcB in Stenotrophomonas chelatiphaga DSM 21508

Align malate synthase A (EC 2.3.3.9) (characterized)
to candidate WP_057509261.1 ABB28_RS14270 malate synthase A

Query= ecocyc::MALATE-SYNTHASE
         (533 letters)



>NCBI__GCF_001431535.1:WP_057509261.1
          Length = 545

 Score =  501 bits (1290), Expect = e-146
 Identities = 267/520 (51%), Positives = 338/520 (65%), Gaps = 17/520 (3%)

Query: 21  EKQILTAEAVEFLTELVTHFTPQRNKLLAARIQQQQDIDNGTLPDFISETASIRDADWKI 80
           +  +L A  +  L  L     P R   LAAR+Q+Q   D G LPDF ++TA IR  DWK+
Sbjct: 28  QSALLPAPLLALLVSLHRAVEPGRQARLAARVQRQAFFDQGGLPDFRTDTAPIRAEDWKV 87

Query: 81  RGIPADLEDRRVEITGPVERKMVINALNANVKVFMADFEDSLAPDWNKVIDGQINLRDAV 140
             +PA L DRRVEITGP + KMVINALN+  KVFMADFED+ AP W  ++ GQ +L  AV
Sbjct: 88  APLPAALLDRRVEITGPTDPKMVINALNSGAKVFMADFEDATAPTWGNLLAGQQSLIGAV 147

Query: 141 NGTISYTNEAG-----KIYQLKP--NPAVLICRVRGLHLPEKHVTWRGEAIPGSLFDFAL 193
            G + +T  A      K Y L+P    AVLI R RG HL EKHV   G+ + G LFD A+
Sbjct: 148 RGDLQFTAPASGSKPSKHYSLRPYEERAVLIVRPRGWHLDEKHVLVDGQRLAGGLFDAAV 207

Query: 194 YFFHNYQALLAKGSGPYFYLPKTQSWQEAAWWSEVFSYAEDRFNLPRGTIKATLLIETLP 253
           + +HN + L+A   GPYFYLPK QS +EAA W    S+ E    LP G IK T+LIETLP
Sbjct: 208 FAYHNARTLMANDRGPYFYLPKLQSMEEAALWETALSHIEGMLGLPHGQIKVTVLIETLP 267

Query: 254 AVFQMDEILHALRDHIVGLNCGRWDYIFSYIKTLKNYPDRVLPDRQAVTMDKPFLNAYSR 313
           AVF+MDEILHALRD IVGLNCGRWDYIFSY+KT + + D+VLP+R  VTM +PFL AYS 
Sbjct: 268 AVFEMDEILHALRDRIVGLNCGRWDYIFSYLKTFRRHADKVLPERGQVTMTQPFLKAYSE 327

Query: 314 LLIKTCHKRGAFAMGGMAAFIP-SKDEEHNNQVLNKVKADKSLEANNGHDGTWIAHPGLA 372
           LLI+TCH+RGA AMGGMAA IP   D   N Q + +V+ADK  E   GHDGTW+AHP L 
Sbjct: 328 LLIQTCHRRGAHAMGGMAAQIPIGNDAAANEQAMARVRADKLREVTAGHDGTWVAHPALI 387

Query: 373 DTAMAVFNDILGSRKNQLEVMREQDAPITADQLLAPCDGERTEEGMRANIRVAVQYIEAW 432
             AMA+F++ +    NQ +V+R QD  +  DQL+A   G  +  G   N+ V V+Y+ AW
Sbjct: 388 PVAMAIFDEHMPG-ANQQQVLR-QDVRVDRDQLIARPPGSISRAGFEGNVEVCVRYLAAW 445

Query: 433 ISGNGCVPIYGLMEDAATAEISRTSIWQWIHHQ-KTLSNGKPVTKALFRQMLGEEMKVIA 491
           + GNGCVPI+ LMEDAATAEISR+ +WQW+H   + L +G  +  AL    L +    + 
Sbjct: 446 LDGNGCVPIHNLMEDAATAEISRSQLWQWLHTPGQQLDDGTAIDAALLDNALAQ----LP 501

Query: 492 SELGEERF--SQGRFDDAARLMEQITTSDELIDFLTLPGY 529
           + LG+       GR D+A  L+ +++ +DEL DFLTLP Y
Sbjct: 502 ARLGDRATLPGGGRVDEAIALLAELSRADELNDFLTLPAY 541


Lambda     K      H
   0.320    0.135    0.407 

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: 776
Number of extensions: 34
Number of successful extensions: 5
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: 533
Length of database: 545
Length adjustment: 35
Effective length of query: 498
Effective length of database: 510
Effective search space:   253980
Effective search space used:   253980
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_057509261.1 ABB28_RS14270 (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.31932.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.3e-211  687.5   0.0   4.9e-211  687.3   0.0    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057509261.1  ABB28_RS14270 malate synthase A


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057509261.1  ABB28_RS14270 malate synthase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  687.3   0.0  4.9e-211  4.9e-211       5     510 ..      35     544 ..      31     545 .] 0.97

  Alignments for each domain:
  == domain 1  score: 687.3 bits;  conditional E-value: 4.9e-211
                                 TIGR01344   5 ealeflaelhrrfaerrkellarrekkqakldkgelldflpetkeireddwkvaaipadlldrrveitG 73 
                                                 l++l++lhr  ++ r++ la+r ++qa +d+g l+df  +t+ ir++dwkva++pa+lldrrveitG
  lcl|NCBI__GCF_001431535.1:WP_057509261.1  35 PLLALLVSLHRAVEPGRQARLAARVQRQAFFDQGGLPDFRTDTAPIRAEDWKVAPLPAALLDRRVEITG 103
                                               568899*************************************************************** PP

                                 TIGR01344  74 PvdrkmvinalnaeakvfladfedsssPtwenvveGqinlkdairgeidftdeesg....keyalk..a 136
                                               P+d kmvinaln++akvf+adfed+++Ptw n++ Gq +l  a+rg+++ft++ sg    k+y l+   
  lcl|NCBI__GCF_001431535.1:WP_057509261.1 104 PTDPKMVINALNSGAKVFMADFEDATAPTWGNLLAGQQSLIGAVRGDLQFTAPASGskpsKHYSLRpyE 172
                                               ***************************************************9765433339*****777 PP

                                 TIGR01344 137 klavlivrprGwhlkerhleidgkaisgslldfglyffhnarellkkGkGPyfylPkleshlearlwnd 205
                                               ++avlivrprGwhl e+h+ +dg+ ++g l+d +++++hnar+l+++ +GPyfylPkl+s  ea lw+ 
  lcl|NCBI__GCF_001431535.1:WP_057509261.1 173 ERAVLIVRPRGWHLDEKHVLVDGQRLAGGLFDAAVFAYHNARTLMANDRGPYFYLPKLQSMEEAALWET 241
                                               99******************************************************************* PP

                                 TIGR01344 206 vfllaqevlglprGtikatvlietlpaafemdeilyelrehssGlncGrwdyifslikklkkaeevvlP 274
                                                +   + +lglp+G ik tvlietlpa+femdeil+ lr+ ++GlncGrwdyifs++k+++++ ++vlP
  lcl|NCBI__GCF_001431535.1:WP_057509261.1 242 ALSHIEGMLGLPHGQIKVTVLIETLPAVFEMDEILHALRDRIVGLNCGRWDYIFSYLKTFRRHADKVLP 310
                                               ********************************************************************* PP

                                 TIGR01344 275 drdavtmdkaflnaysklliqtchrrgafalGGmaafiPikddpaaneaalekvradkereaknGhdGt 343
                                               +r +vtm+++fl+ays+lliqtchrrga+a+GGmaa+iPi +d+aane+a+++vradk re+++GhdGt
  lcl|NCBI__GCF_001431535.1:WP_057509261.1 311 ERGQVTMTQPFLKAYSELLIQTCHRRGAHAMGGMAAQIPIGNDAAANEQAMARVRADKLREVTAGHDGT 379
                                               ********************************************************************* PP

                                 TIGR01344 344 wvahPdlvevalevfdevlgepnqldrvrledvsitaaellevkdasrteeGlrenirvglryieawlr 412
                                               wvahP+l++va+++fde+++ +nq +++r +dv++ + +l++ + +s + +G+  n++v +ry++awl+
  lcl|NCBI__GCF_001431535.1:WP_057509261.1 380 WVAHPALIPVAMAIFDEHMPGANQQQVLR-QDVRVDRDQLIARPPGSISRAGFEGNVEVCVRYLAAWLD 447
                                               ***************************99.9************************************** PP

                                 TIGR01344 413 GsGavpiynlmedaataeisraqlwqwikh.GvvledGekvtselvrdllkeeleklkkesgkeeyaka 480
                                               G+G+vpi+nlmedaataeisr+qlwqw+++ G+ l+dG  + ++l+ ++l++  ++l + ++    + +
  lcl|NCBI__GCF_001431535.1:WP_057509261.1 448 GNGCVPIHNLMEDAATAEISRSQLWQWLHTpGQQLDDGTAIDAALLDNALAQLPARLGDRATLP--GGG 514
                                               ****************************9669*************************9996665..599 PP

                                 TIGR01344 481 rleeaaellerlvlseeledfltlpaydel 510
                                               r++ea  ll +l+ ++el+dfltlpay ++
  lcl|NCBI__GCF_001431535.1:WP_057509261.1 515 RVDEAIALLAELSRADELNDFLTLPAYARI 544
                                               ***************************886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (511 nodes)
Target sequences:                          1  (545 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: 13.00
//
[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)
Rules (tab-delimited)
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 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