GapMind for catabolism of small carbon sources

 

Alignments for a candidate for garD in Escherichia coli BW25113

Align Galactarate dehydratase (L-threo-forming); GalcD; EC 4.2.1.42 (characterized)
to candidate 17201 b3128 (D)-galactarate dehydrogenase (NCBI)

Query= SwissProt::P39829
         (523 letters)



>FitnessBrowser__Keio:17201
          Length = 523

 Score = 1048 bits (2710), Expect = 0.0
 Identities = 523/523 (100%), Positives = 523/523 (100%)

Query: 1   MANIEIRQETPTAFYIKVHDTDNVAIIVNDNGLKAGTRFPDGLELIEHIPQGHKVALLDI 60
           MANIEIRQETPTAFYIKVHDTDNVAIIVNDNGLKAGTRFPDGLELIEHIPQGHKVALLDI
Sbjct: 1   MANIEIRQETPTAFYIKVHDTDNVAIIVNDNGLKAGTRFPDGLELIEHIPQGHKVALLDI 60

Query: 61  PANGEIIRYGEVIGYAVRAIPRGSWIDESMVVLPEAPPLHTLPLATKVPEPLPPLEGYTF 120
           PANGEIIRYGEVIGYAVRAIPRGSWIDESMVVLPEAPPLHTLPLATKVPEPLPPLEGYTF
Sbjct: 61  PANGEIIRYGEVIGYAVRAIPRGSWIDESMVVLPEAPPLHTLPLATKVPEPLPPLEGYTF 120

Query: 121 EGYRNADGSVGTKNLLGITTSVHCVAGVVDYVVKIIERDLLPKYPNVDGVVGLNHLYGCG 180
           EGYRNADGSVGTKNLLGITTSVHCVAGVVDYVVKIIERDLLPKYPNVDGVVGLNHLYGCG
Sbjct: 121 EGYRNADGSVGTKNLLGITTSVHCVAGVVDYVVKIIERDLLPKYPNVDGVVGLNHLYGCG 180

Query: 181 VAINAPAAVVPIRTIHNISLNPNFGGEVMVIGLGCEKLQPERLLTGTDDVQAIPVESASI 240
           VAINAPAAVVPIRTIHNISLNPNFGGEVMVIGLGCEKLQPERLLTGTDDVQAIPVESASI
Sbjct: 181 VAINAPAAVVPIRTIHNISLNPNFGGEVMVIGLGCEKLQPERLLTGTDDVQAIPVESASI 240

Query: 241 VSLQDEKHVGFQSMVEDILQIAERHLQKLNQRQRETCPASELVVGMQCGGSDAFSGVTAN 300
           VSLQDEKHVGFQSMVEDILQIAERHLQKLNQRQRETCPASELVVGMQCGGSDAFSGVTAN
Sbjct: 241 VSLQDEKHVGFQSMVEDILQIAERHLQKLNQRQRETCPASELVVGMQCGGSDAFSGVTAN 300

Query: 301 PAVGYASDLLVRCGATVMFSEVTEVRDAIHLLTPRAVNEEVGKRLLEEMEWYDNYLNMGK 360
           PAVGYASDLLVRCGATVMFSEVTEVRDAIHLLTPRAVNEEVGKRLLEEMEWYDNYLNMGK
Sbjct: 301 PAVGYASDLLVRCGATVMFSEVTEVRDAIHLLTPRAVNEEVGKRLLEEMEWYDNYLNMGK 360

Query: 361 TDRSANPSPGNKKGGLANVVEKALGSIAKSGKSAIVEVLSPGQRPTKRGLIYAATPASDF 420
           TDRSANPSPGNKKGGLANVVEKALGSIAKSGKSAIVEVLSPGQRPTKRGLIYAATPASDF
Sbjct: 361 TDRSANPSPGNKKGGLANVVEKALGSIAKSGKSAIVEVLSPGQRPTKRGLIYAATPASDF 420

Query: 421 VCGTQQVASGITVQVFTTGRGTPYGLMAVPVIKMATRTELANRWFDLMDINAGTIATGEE 480
           VCGTQQVASGITVQVFTTGRGTPYGLMAVPVIKMATRTELANRWFDLMDINAGTIATGEE
Sbjct: 421 VCGTQQVASGITVQVFTTGRGTPYGLMAVPVIKMATRTELANRWFDLMDINAGTIATGEE 480

Query: 481 TIEEVGWKLFHFILDVASGKKKTFSDQWGLHNQLAVFNPAPVT 523
           TIEEVGWKLFHFILDVASGKKKTFSDQWGLHNQLAVFNPAPVT
Sbjct: 481 TIEEVGWKLFHFILDVASGKKKTFSDQWGLHNQLAVFNPAPVT 523


Lambda     K      H
   0.317    0.136    0.403 

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: 1071
Number of extensions: 32
Number of successful extensions: 3
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: 523
Length of database: 523
Length adjustment: 35
Effective length of query: 488
Effective length of database: 488
Effective search space:   238144
Effective search space used:   238144
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: 52 (24.6 bits)

Align candidate 17201 b3128 ((D)-galactarate dehydrogenase (NCBI))
to HMM TIGR03248 (garD: galactarate dehydratase (EC 4.2.1.42))

# 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/TIGR03248.hmm
# target sequence database:        /tmp/gapView.372346.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03248  [M=507]
Accession:   TIGR03248
Description: galactar-dH20: galactarate dehydratase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   9.3e-288  940.6   0.1   1.1e-287  940.4   0.1    1.0  1  lcl|FitnessBrowser__Keio:17201  b3128 (D)-galactarate dehydrogen


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:17201  b3128 (D)-galactarate dehydrogenase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  940.4   0.1  1.1e-287  1.1e-287       2     507 .]      15     523 .]      14     523 .] 0.99

  Alignments for each domain:
  == domain 1  score: 940.4 bits;  conditional E-value: 1.1e-287
                       TIGR03248   2 yirvneqdnvaivvndkGlpagtefedgltlvekipqghkvalvdlekgdaiirygeviGyavkdiarGswvkeellel 80 
                                     yi+v+++dnvai+vnd+Gl agt+f+dgl+l+e+ipqghkval d+ ++ +iirygeviGyav++i+rGsw++e+++ l
  lcl|FitnessBrowser__Keio:17201  15 YIKVHDTDNVAIIVNDNGLKAGTRFPDGLELIEHIPQGHKVALLDIPANGEIIRYGEVIGYAVRAIPRGSWIDESMVVL 93 
                                     9****************************************************************************** PP

                       TIGR03248  81 psapaleelplatkvpeklapleGytfeGyrnadGsvGtknilgittsvqcvagvvdyavkrikkellpkypnvddvva 159
                                     p+ap+l++lplatkvpe+l+pleGytfeGyrnadGsvGtkn+lgittsv+cvagvvdy+vk i+++llpkypnvd+vv+
  lcl|FitnessBrowser__Keio:17201  94 PEAPPLHTLPLATKVPEPLPPLEGYTFEGYRNADGSVGTKNLLGITTSVHCVAGVVDYVVKIIERDLLPKYPNVDGVVG 172
                                     ******************************************************************************* PP

                       TIGR03248 160 lnhsyGcGvaidapdaivpirtlrnlalnpnlGGealvvglGceklqperllp..eelsavelkdaavlrlqdekl.Gf 235
                                     lnh yGcGvai+ap+a+vpirt++n++lnpn+GGe++v+glGceklqperll+  ++++a+ ++ a++++lqdek+ Gf
  lcl|FitnessBrowser__Keio:17201 173 LNHLYGCGVAINAPAAVVPIRTIHNISLNPNFGGEVMVIGLGCEKLQPERLLTgtDDVQAIPVESASIVSLQDEKHvGF 251
                                     ***************************************************963256677999**************** PP

                       TIGR03248 236 aemveailelaeerlkklnarkretvpaselvvGlqcGGsdafsGvtanpavGfaadllvraGatvlfsevtevrdaih 314
                                     ++mve+il++ae++l+kln+r+ret+paselvvG+qcGGsdafsGvtanpavG+a+dllvr Gatv+fsevtevrdaih
  lcl|FitnessBrowser__Keio:17201 252 QSMVEDILQIAERHLQKLNQRQRETCPASELVVGMQCGGSDAFSGVTANPAVGYASDLLVRCGATVMFSEVTEVRDAIH 330
                                     ******************************************************************************* PP

                       TIGR03248 315 lltpraedaevakaliremkwydeylarGeadrsanttpGnkkGGlsnivekalGsivksGssaivevlspGekvkkkG 393
                                     lltpra ++ev+k+l++em+wyd+yl++G++drsan++pGnkkGGl+n+vekalGsi+ksG saivevlspG++++k+G
  lcl|FitnessBrowser__Keio:17201 331 LLTPRAVNEEVGKRLLEEMEWYDNYLNMGKTDRSANPSPGNKKGGLANVVEKALGSIAKSGKSAIVEVLSPGQRPTKRG 409
                                     ******************************************************************************* PP

                       TIGR03248 394 liyaatpasdfvcGtlqlasglnlhvfttGrGtpyGlalvpvikvstrtelaerwadlidldaGriatGeatiedvGwe 472
                                     liyaatpasdfvcGt+q+asg++++vfttGrGtpyGl +vpvik++trtela+rw+dl+d++aG+iatGe+tie+vGw+
  lcl|FitnessBrowser__Keio:17201 410 LIYAATPASDFVCGTQQVASGITVQVFTTGRGTPYGLMAVPVIKMATRTELANRWFDLMDINAGTIATGEETIEEVGWK 488
                                     ******************************************************************************* PP

                       TIGR03248 473 lfrlildvasGrkktwaekyklhndlalfnpapvt 507
                                     lf++ildvasG+kkt++++++lhn+la+fnpapvt
  lcl|FitnessBrowser__Keio:17201 489 LFHFILDVASGKKKTFSDQWGLHNQLAVFNPAPVT 523
                                     **********************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (507 nodes)
Target sequences:                          1  (523 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 18.69
//
[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