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 G; MSG; EC 2.3.3.9 (characterized)
to candidate 17054 b2976 malate synthase (NCBI)

Query= SwissProt::P37330
         (723 letters)



>FitnessBrowser__Keio:17054
          Length = 723

 Score = 1449 bits (3750), Expect = 0.0
 Identities = 723/723 (100%), Positives = 723/723 (100%)

Query: 1   MSQTITQSRLRIDANFKRFVDEEVLPGTGLDAAAFWRNFDEIVHDLAPENRQLLAERDRI 60
           MSQTITQSRLRIDANFKRFVDEEVLPGTGLDAAAFWRNFDEIVHDLAPENRQLLAERDRI
Sbjct: 1   MSQTITQSRLRIDANFKRFVDEEVLPGTGLDAAAFWRNFDEIVHDLAPENRQLLAERDRI 60

Query: 61  QAALDEWHRSNPGPVKDKAAYKSFLRELGYLVPQPERVTVETTGIDSEITSQAGPQLVVP 120
           QAALDEWHRSNPGPVKDKAAYKSFLRELGYLVPQPERVTVETTGIDSEITSQAGPQLVVP
Sbjct: 61  QAALDEWHRSNPGPVKDKAAYKSFLRELGYLVPQPERVTVETTGIDSEITSQAGPQLVVP 120

Query: 121 AMNARYALNAANARWGSLYDALYGSDIIPQEGAMVSGYDPQRGEQVIAWVRRFLDESLPL 180
           AMNARYALNAANARWGSLYDALYGSDIIPQEGAMVSGYDPQRGEQVIAWVRRFLDESLPL
Sbjct: 121 AMNARYALNAANARWGSLYDALYGSDIIPQEGAMVSGYDPQRGEQVIAWVRRFLDESLPL 180

Query: 181 ENGSYQDVVAFKVVDKQLRIQLKNGKETTLRTPAQFVGYRGDAAAPTCILLKNNGLHIEL 240
           ENGSYQDVVAFKVVDKQLRIQLKNGKETTLRTPAQFVGYRGDAAAPTCILLKNNGLHIEL
Sbjct: 181 ENGSYQDVVAFKVVDKQLRIQLKNGKETTLRTPAQFVGYRGDAAAPTCILLKNNGLHIEL 240

Query: 241 QIDANGRIGKDDPAHINDVIVEAAISTILDCEDSVAAVDAEDKILLYRNLLGLMQGTLQE 300
           QIDANGRIGKDDPAHINDVIVEAAISTILDCEDSVAAVDAEDKILLYRNLLGLMQGTLQE
Sbjct: 241 QIDANGRIGKDDPAHINDVIVEAAISTILDCEDSVAAVDAEDKILLYRNLLGLMQGTLQE 300

Query: 301 KMEKNGRQIVRKLNDDRHYTAADGSEISLHGRSLLFIRNVGHLMTIPVIWDSEGNEIPEG 360
           KMEKNGRQIVRKLNDDRHYTAADGSEISLHGRSLLFIRNVGHLMTIPVIWDSEGNEIPEG
Sbjct: 301 KMEKNGRQIVRKLNDDRHYTAADGSEISLHGRSLLFIRNVGHLMTIPVIWDSEGNEIPEG 360

Query: 361 ILDGVMTGAIALYDLKVQKNSRTGSVYIVKPKMHGPQEVAFANKLFTRIETMLGMAPNTL 420
           ILDGVMTGAIALYDLKVQKNSRTGSVYIVKPKMHGPQEVAFANKLFTRIETMLGMAPNTL
Sbjct: 361 ILDGVMTGAIALYDLKVQKNSRTGSVYIVKPKMHGPQEVAFANKLFTRIETMLGMAPNTL 420

Query: 421 KMGIMDEERRTSLNLRSCIAQARNRVAFINTGFLDRTGDEMHSVMEAGPMLRKNQMKSTP 480
           KMGIMDEERRTSLNLRSCIAQARNRVAFINTGFLDRTGDEMHSVMEAGPMLRKNQMKSTP
Sbjct: 421 KMGIMDEERRTSLNLRSCIAQARNRVAFINTGFLDRTGDEMHSVMEAGPMLRKNQMKSTP 480

Query: 481 WIKAYERNNVLSGLFCGLRGKAQIGKGMWAMPDLMADMYSQKGDQLRAGANTAWVPSPTA 540
           WIKAYERNNVLSGLFCGLRGKAQIGKGMWAMPDLMADMYSQKGDQLRAGANTAWVPSPTA
Sbjct: 481 WIKAYERNNVLSGLFCGLRGKAQIGKGMWAMPDLMADMYSQKGDQLRAGANTAWVPSPTA 540

Query: 541 ATLHALHYHQTNVQSVQANIAQTEFNAEFEPLLDDLLTIPVAENANWSAQEIQQELDNNV 600
           ATLHALHYHQTNVQSVQANIAQTEFNAEFEPLLDDLLTIPVAENANWSAQEIQQELDNNV
Sbjct: 541 ATLHALHYHQTNVQSVQANIAQTEFNAEFEPLLDDLLTIPVAENANWSAQEIQQELDNNV 600

Query: 601 QGILGYVVRWVEQGIGCSKVPDIHNVALMEDRATLRISSQHIANWLRHGILTKEQVQASL 660
           QGILGYVVRWVEQGIGCSKVPDIHNVALMEDRATLRISSQHIANWLRHGILTKEQVQASL
Sbjct: 601 QGILGYVVRWVEQGIGCSKVPDIHNVALMEDRATLRISSQHIANWLRHGILTKEQVQASL 660

Query: 661 ENMAKVVDQQNAGDPAYRPMAGNFANSCAFKAASDLIFLGVKQPNGYTEPLLHAWRLREK 720
           ENMAKVVDQQNAGDPAYRPMAGNFANSCAFKAASDLIFLGVKQPNGYTEPLLHAWRLREK
Sbjct: 661 ENMAKVVDQQNAGDPAYRPMAGNFANSCAFKAASDLIFLGVKQPNGYTEPLLHAWRLREK 720

Query: 721 ESH 723
           ESH
Sbjct: 721 ESH 723


Lambda     K      H
   0.318    0.134    0.394 

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: 1808
Number of extensions: 61
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: 723
Length of database: 723
Length adjustment: 40
Effective length of query: 683
Effective length of database: 683
Effective search space:   466489
Effective search space used:   466489
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)

Align candidate 17054 b2976 (malate synthase (NCBI))
to HMM TIGR01345 (glcB: malate synthase G (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/TIGR01345.hmm
# target sequence database:        /tmp/gapView.27152.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01345  [M=721]
Accession:   TIGR01345
Description: malate_syn_G: malate synthase G
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
          0 1434.0   0.2          0 1433.8   0.2    1.0  1  lcl|FitnessBrowser__Keio:17054  b2976 malate synthase (NCBI)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:17054  b2976 malate synthase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1433.8   0.2         0         0       1     721 []       3     723 .]       3     723 .] 0.99

  Alignments for each domain:
  == domain 1  score: 1433.8 bits;  conditional E-value: 0
                       TIGR01345   1 ervdagrlqvakklkdfveeevlpgtgvdaekfwsgfdeivrdlapenrellakrdeiqaaideyhrknk.gvidkeay 78 
                                     ++++++rl++++++k+fv+eevlpgtg+da++fw++fdeiv+dlapenr+lla+rd+iqaa+de+hr+n+ +v+dk+ay
  lcl|FitnessBrowser__Keio:17054   3 QTITQSRLRIDANFKRFVDEEVLPGTGLDAAAFWRNFDEIVHDLAPENRQLLAERDRIQAALDEWHRSNPgPVKDKAAY 81 
                                     5899******************************************************************7899***** PP

                       TIGR01345  79 ksflkeigylveepervtietenvdseiasqagpqlvvpvlnaryalnaanarwgslydalygsnvipeedgaekgkey 157
                                     ksfl+e+gylv++pervt+et+++dsei+sqagpqlvvp++naryalnaanarwgslydalygs++ip+e+++++g  y
  lcl|FitnessBrowser__Keio:17054  82 KSFLRELGYLVPQPERVTVETTGIDSEITSQAGPQLVVPAMNARYALNAANARWGSLYDALYGSDIIPQEGAMVSG--Y 158
                                     ****************************************************************************..* PP

                       TIGR01345 158 npkrgekviefarefldeslplesgsyadvvkykivdkklavqlesgkvtrlkdeeqfvgyrgdaadpevillktnglh 236
                                     +p+rge+vi+++r+fldeslple+gsy+dvv++k+vdk+l++ql++gk+t+l++++qfvgyrgdaa+p++illk+nglh
  lcl|FitnessBrowser__Keio:17054 159 DPQRGEQVIAWVRRFLDESLPLENGSYQDVVAFKVVDKQLRIQLKNGKETTLRTPAQFVGYRGDAAAPTCILLKNNGLH 237
                                     ******************************************************************************* PP

                       TIGR01345 237 ielqidarhpigkadkakvkdivlesaittildcedsvaavdaedkvlvyrnllglmkgtlkeklekngriikrklned 315
                                     ielqida+++igk+d+a+++d+++e+ai+tildcedsvaavdaedk+l+yrnllglm+gtl+ek+ekngr+i+rkln+d
  lcl|FitnessBrowser__Keio:17054 238 IELQIDANGRIGKDDPAHINDVIVEAAISTILDCEDSVAAVDAEDKILLYRNLLGLMQGTLQEKMEKNGRQIVRKLNDD 316
                                     ******************************************************************************* PP

                       TIGR01345 316 rsytaangeelslhgrsllfvrnvghlmtipviltdegeeipegildgvltsvialydlkvqnklrnsrkgsvyivkpk 394
                                     r+ytaa+g+e+slhgrsllf+rnvghlmtipvi+++eg+eipegildgv+t++ialydlkvq   +nsr+gsvyivkpk
  lcl|FitnessBrowser__Keio:17054 317 RHYTAADGSEISLHGRSLLFIRNVGHLMTIPVIWDSEGNEIPEGILDGVMTGAIALYDLKVQ---KNSRTGSVYIVKPK 392
                                     *************************************************************5...6************* PP

                       TIGR01345 395 mhgpeevafanklftriedllglerhtlkvgvmdeerrtslnlkaciakvkervafintgfldrtgdeihtsmeagamv 473
                                     mhgp+evafanklftrie++lg++++tlk+g+mdeerrtslnl++cia++++rvafintgfldrtgde+h++meag+m+
  lcl|FitnessBrowser__Keio:17054 393 MHGPQEVAFANKLFTRIETMLGMAPNTLKMGIMDEERRTSLNLRSCIAQARNRVAFINTGFLDRTGDEMHSVMEAGPML 471
                                     ******************************************************************************* PP

                       TIGR01345 474 rkadmksapwlkayernnvaagltcglrgkaqigkgmwampdlmaemlekkgdqlragantawvpsptaatlhalhyhr 552
                                     rk++mks+pw+kayernnv++gl+cglrgkaqigkgmwampdlma+m+++kgdqlragantawvpsptaatlhalhyh+
  lcl|FitnessBrowser__Keio:17054 472 RKNQMKSTPWIKAYERNNVLSGLFCGLRGKAQIGKGMWAMPDLMADMYSQKGDQLRAGANTAWVPSPTAATLHALHYHQ 550
                                     ******************************************************************************* PP

                       TIGR01345 553 vdvqkvqkeladaerrae....lkeiltipvaentnwseeeikeeldnnvqgilgyvvrwveqgigcskvpdihnvalm 627
                                     ++vq+vq+++a++e++ae    l+++ltipvaen+nws++ei++eldnnvqgilgyvvrwveqgigcskvpdihnvalm
  lcl|FitnessBrowser__Keio:17054 551 TNVQSVQANIAQTEFNAEfeplLDDLLTIPVAENANWSAQEIQQELDNNVQGILGYVVRWVEQGIGCSKVPDIHNVALM 629
                                     *****************999999******************************************************** PP

                       TIGR01345 628 edratlrissqhlanwlrhgivskeqvleslermakvvdkqnagdeayrpmadnleasvafkaakdlilkgtkqpsgyt 706
                                     edratlrissqh+anwlrhgi++keqv++sle+makvvd+qnagd+ayrpma+n+++s+afkaa+dli+ g+kqp+gyt
  lcl|FitnessBrowser__Keio:17054 630 EDRATLRISSQHIANWLRHGILTKEQVQASLENMAKVVDQQNAGDPAYRPMAGNFANSCAFKAASDLIFLGVKQPNGYT 708
                                     ******************************************************************************* PP

                       TIGR01345 707 epilharrlefkekn 721
                                     ep+lha+rl++ke++
  lcl|FitnessBrowser__Keio:17054 709 EPLLHAWRLREKESH 723
                                     ************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (721 nodes)
Target sequences:                          1  (723 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: 0.03u 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 10.57
//
[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