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.3218.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: 9.95
//
[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:

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:

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:

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:

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