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.5723.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: 12.11
//
[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