Alignments for a candidate for glcB in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for glcB in Escherichia coli BW25113

Align malate synthase A (EC 2.3.3.9) (characterized)
to candidate 18042 b4014 malate synthase (NCBI)

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



>FitnessBrowser__Keio:18042
          Length = 533

 Score = 1080 bits (2794), Expect = 0.0
 Identities = 533/533 (100%), Positives = 533/533 (100%)

Query: 1   MTEQATTTDELAFTRPYGEQEKQILTAEAVEFLTELVTHFTPQRNKLLAARIQQQQDIDN 60
           MTEQATTTDELAFTRPYGEQEKQILTAEAVEFLTELVTHFTPQRNKLLAARIQQQQDIDN
Sbjct: 1   MTEQATTTDELAFTRPYGEQEKQILTAEAVEFLTELVTHFTPQRNKLLAARIQQQQDIDN 60

Query: 61  GTLPDFISETASIRDADWKIRGIPADLEDRRVEITGPVERKMVINALNANVKVFMADFED 120
           GTLPDFISETASIRDADWKIRGIPADLEDRRVEITGPVERKMVINALNANVKVFMADFED
Sbjct: 61  GTLPDFISETASIRDADWKIRGIPADLEDRRVEITGPVERKMVINALNANVKVFMADFED 120

Query: 121 SLAPDWNKVIDGQINLRDAVNGTISYTNEAGKIYQLKPNPAVLICRVRGLHLPEKHVTWR 180
           SLAPDWNKVIDGQINLRDAVNGTISYTNEAGKIYQLKPNPAVLICRVRGLHLPEKHVTWR
Sbjct: 121 SLAPDWNKVIDGQINLRDAVNGTISYTNEAGKIYQLKPNPAVLICRVRGLHLPEKHVTWR 180

Query: 181 GEAIPGSLFDFALYFFHNYQALLAKGSGPYFYLPKTQSWQEAAWWSEVFSYAEDRFNLPR 240
           GEAIPGSLFDFALYFFHNYQALLAKGSGPYFYLPKTQSWQEAAWWSEVFSYAEDRFNLPR
Sbjct: 181 GEAIPGSLFDFALYFFHNYQALLAKGSGPYFYLPKTQSWQEAAWWSEVFSYAEDRFNLPR 240

Query: 241 GTIKATLLIETLPAVFQMDEILHALRDHIVGLNCGRWDYIFSYIKTLKNYPDRVLPDRQA 300
           GTIKATLLIETLPAVFQMDEILHALRDHIVGLNCGRWDYIFSYIKTLKNYPDRVLPDRQA
Sbjct: 241 GTIKATLLIETLPAVFQMDEILHALRDHIVGLNCGRWDYIFSYIKTLKNYPDRVLPDRQA 300

Query: 301 VTMDKPFLNAYSRLLIKTCHKRGAFAMGGMAAFIPSKDEEHNNQVLNKVKADKSLEANNG 360
           VTMDKPFLNAYSRLLIKTCHKRGAFAMGGMAAFIPSKDEEHNNQVLNKVKADKSLEANNG
Sbjct: 301 VTMDKPFLNAYSRLLIKTCHKRGAFAMGGMAAFIPSKDEEHNNQVLNKVKADKSLEANNG 360

Query: 361 HDGTWIAHPGLADTAMAVFNDILGSRKNQLEVMREQDAPITADQLLAPCDGERTEEGMRA 420
           HDGTWIAHPGLADTAMAVFNDILGSRKNQLEVMREQDAPITADQLLAPCDGERTEEGMRA
Sbjct: 361 HDGTWIAHPGLADTAMAVFNDILGSRKNQLEVMREQDAPITADQLLAPCDGERTEEGMRA 420

Query: 421 NIRVAVQYIEAWISGNGCVPIYGLMEDAATAEISRTSIWQWIHHQKTLSNGKPVTKALFR 480
           NIRVAVQYIEAWISGNGCVPIYGLMEDAATAEISRTSIWQWIHHQKTLSNGKPVTKALFR
Sbjct: 421 NIRVAVQYIEAWISGNGCVPIYGLMEDAATAEISRTSIWQWIHHQKTLSNGKPVTKALFR 480

Query: 481 QMLGEEMKVIASELGEERFSQGRFDDAARLMEQITTSDELIDFLTLPGYRLLA 533
           QMLGEEMKVIASELGEERFSQGRFDDAARLMEQITTSDELIDFLTLPGYRLLA
Sbjct: 481 QMLGEEMKVIASELGEERFSQGRFDDAARLMEQITTSDELIDFLTLPGYRLLA 533


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: 1086
Number of extensions: 27
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: 533
Length of database: 533
Length adjustment: 35
Effective length of query: 498
Effective length of database: 498
Effective search space:   248004
Effective search space used:   248004
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 18042 b4014 (malate synthase (NCBI))
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.18949.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-254  831.2   0.0   1.3e-254  831.1   0.0    1.0  1  lcl|FitnessBrowser__Keio:18042  b4014 malate synthase (NCBI)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:18042  b4014 malate synthase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  831.1   0.0  1.3e-254  1.3e-254       1     510 [.      24     532 ..      24     533 .] 0.99

  Alignments for each domain:
  == domain 1  score: 831.1 bits;  conditional E-value: 1.3e-254
                       TIGR01344   1 vltkealeflaelhrrfaerrkellarrekkqakldkgelldflpetkeireddwkvaaipadlldrrveitGPvdrkm 79 
                                     +lt ea+efl+el  +f+++r++lla+r ++q  +d+g+l+df+ et++ir++dwk+  ipadl drrveitGPv+rkm
  lcl|FitnessBrowser__Keio:18042  24 ILTAEAVEFLTELVTHFTPQRNKLLAARIQQQQDIDNGTLPDFISETASIRDADWKIRGIPADLEDRRVEITGPVERKM 102
                                     79***************************************************************************** PP

                       TIGR01344  80 vinalnaeakvfladfedsssPtwenvveGqinlkdairgeidftdeesgkeyalkaklavlivrprGwhlkerhleid 158
                                     vinalna++kvf+adfeds +P w++v++Gqinl+da++g+i++t+ e+gk y+lk++ avli+r+rG+hl+e+h++  
  lcl|FitnessBrowser__Keio:18042 103 VINALNANVKVFMADFEDSLAPDWNKVIDGQINLRDAVNGTISYTN-EAGKIYQLKPNPAVLICRVRGLHLPEKHVTWR 180
                                     *********************************************7.99****************************** PP

                       TIGR01344 159 gkaisgslldfglyffhnarellkkGkGPyfylPkleshlearlwndvfllaqevlglprGtikatvlietlpaafemd 237
                                     g+ai+gsl+df+lyffhn ++ll+kG+GPyfylPk +s++ea +w++vf +a++ ++lprGtikat+lietlpa+f+md
  lcl|FitnessBrowser__Keio:18042 181 GEAIPGSLFDFALYFFHNYQALLAKGSGPYFYLPKTQSWQEAAWWSEVFSYAEDRFNLPRGTIKATLLIETLPAVFQMD 259
                                     ******************************************************************************* PP

                       TIGR01344 238 eilyelrehssGlncGrwdyifslikklkkaeevvlPdrdavtmdkaflnaysklliqtchrrgafalGGmaafiPikd 316
                                     eil+ lr+h++GlncGrwdyifs+ik+lk+ +++vlPdr+avtmdk+flnays+lli+tch+rgafa+GGmaafiP+k 
  lcl|FitnessBrowser__Keio:18042 260 EILHALRDHIVGLNCGRWDYIFSYIKTLKNYPDRVLPDRQAVTMDKPFLNAYSRLLIKTCHKRGAFAMGGMAAFIPSK- 337
                                     ******************************************************************************. PP

                       TIGR01344 317 dpaaneaalekvradkereaknGhdGtwvahPdlvevalevfdevlge.pnqldrvrledvsitaaellevkdasrtee 394
                                     d++ n+++l+kv+adk +ea+nGhdGtw+ahP+l+++a++vf+++lg+ +nql+++r++d++ita +ll+ +d++rtee
  lcl|FitnessBrowser__Keio:18042 338 DEEHNNQVLNKVKADKSLEANNGHDGTWIAHPGLADTAMAVFNDILGSrKNQLEVMREQDAPITADQLLAPCDGERTEE 416
                                     999********************************************99****************************** PP

                       TIGR01344 395 GlrenirvglryieawlrGsGavpiynlmedaataeisraqlwqwikhGvvledGekvtselvrdllkeeleklkkesg 473
                                     G+r nirv+++yieaw++G+G+vpiy lmedaataeisr+++wqwi+h ++l++G+ vt++l+r++l ee++ +++e+g
  lcl|FitnessBrowser__Keio:18042 417 GMRANIRVAVQYIEAWISGNGCVPIYGLMEDAATAEISRTSIWQWIHHQKTLSNGKPVTKALFRQMLGEEMKVIASELG 495
                                     ******************************************************************************* PP

                       TIGR01344 474 keeyakarleeaaellerlvlseeledfltlpaydel 510
                                     +e+++++r++ aa+l+e++++s+el dfltlp+y  l
  lcl|FitnessBrowser__Keio:18042 496 EERFSQGRFDDAARLMEQITTSDELIDFLTLPGYRLL 532
                                     **********************************876 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 11.05
//
[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