Alignments for a candidate for garD in Escherichia coli BW25113

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.32141.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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.02
# Mc/sec: 9.01
//
[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