Alignments for a candidate for garD in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for garD in Pseudomonas simiae WCS417

Align Galactarate dehydratase (EC 4.2.1.42) (characterized)
to candidate GFF829 PS417_04210 galactarate dehydrogenase

Query= reanno::WCS417:GFF829
         (517 letters)



>FitnessBrowser__WCS417:GFF829
          Length = 517

 Score = 1037 bits (2681), Expect = 0.0
 Identities = 517/517 (100%), Positives = 517/517 (100%)

Query: 1   MQLIEHADSPRSIRLHERDNVVIVVNDQGVPAGTEFPDGLVTVDFIPQSHKVTLEDIPEG 60
           MQLIEHADSPRSIRLHERDNVVIVVNDQGVPAGTEFPDGLVTVDFIPQSHKVTLEDIPEG
Sbjct: 1   MQLIEHADSPRSIRLHERDNVVIVVNDQGVPAGTEFPDGLVTVDFIPQSHKVTLEDIPEG 60

Query: 61  GQIIRYGQTIGYALAPIPRGSWVQEDQLRMPTAPPLDSLPLSTEVPEAQAPLEGFTFEGY 120
           GQIIRYGQTIGYALAPIPRGSWVQEDQLRMPTAPPLDSLPLSTEVPEAQAPLEGFTFEGY
Sbjct: 61  GQIIRYGQTIGYALAPIPRGSWVQEDQLRMPTAPPLDSLPLSTEVPEAQAPLEGFTFEGY 120

Query: 121 RNADGTVGTRNILGITTTVQCVTGVLDHAVKRIKDELLPKYPHVDDVVALTHSYGCGVAI 180
           RNADGTVGTRNILGITTTVQCVTGVLDHAVKRIKDELLPKYPHVDDVVALTHSYGCGVAI
Sbjct: 121 RNADGTVGTRNILGITTTVQCVTGVLDHAVKRIKDELLPKYPHVDDVVALTHSYGCGVAI 180

Query: 181 TATDAYIPIRTVRNLARNPNLGGEALVISLGCEKLQAGQVMHDNDSSVDLSEPWLYRLQD 240
           TATDAYIPIRTVRNLARNPNLGGEALVISLGCEKLQAGQVMHDNDSSVDLSEPWLYRLQD
Sbjct: 181 TATDAYIPIRTVRNLARNPNLGGEALVISLGCEKLQAGQVMHDNDSSVDLSEPWLYRLQD 240

Query: 241 SSHGFTEMIEQIMALAETRLKKLDQRRRETVPASELILGMQCGGSDAFSGITANPALGYA 300
           SSHGFTEMIEQIMALAETRLKKLDQRRRETVPASELILGMQCGGSDAFSGITANPALGYA
Sbjct: 241 SSHGFTEMIEQIMALAETRLKKLDQRRRETVPASELILGMQCGGSDAFSGITANPALGYA 300

Query: 301 SDLLLRAGATVMFSEVTEVRDAIYLLTSRAENTQVAQELVREMDWYDRYLAKGEADRSAN 360
           SDLLLRAGATVMFSEVTEVRDAIYLLTSRAENTQVAQELVREMDWYDRYLAKGEADRSAN
Sbjct: 301 SDLLLRAGATVMFSEVTEVRDAIYLLTSRAENTQVAQELVREMDWYDRYLAKGEADRSAN 360

Query: 361 TTPGNKKGGLSNIVEKSLGSIVKSGSSAINGVLGPGERFKGKGLIFCATPASDFVCGTLQ 420
           TTPGNKKGGLSNIVEKSLGSIVKSGSSAINGVLGPGERFKGKGLIFCATPASDFVCGTLQ
Sbjct: 361 TTPGNKKGGLSNIVEKSLGSIVKSGSSAINGVLGPGERFKGKGLIFCATPASDFVCGTLQ 420

Query: 421 LAAGMNLHVFTTGRGTPYGLAMAPVVKVSTRTELAQRWPDLIDIDAGRIATGRATIEELG 480
           LAAGMNLHVFTTGRGTPYGLAMAPVVKVSTRTELAQRWPDLIDIDAGRIATGRATIEELG
Sbjct: 421 LAAGMNLHVFTTGRGTPYGLAMAPVVKVSTRTELAQRWPDLIDIDAGRIATGRATIEELG 480

Query: 481 WELFHFYLDVASGRKQTWAEHHKLHNDITLFNPAPIT 517
           WELFHFYLDVASGRKQTWAEHHKLHNDITLFNPAPIT
Sbjct: 481 WELFHFYLDVASGRKQTWAEHHKLHNDITLFNPAPIT 517


Lambda     K      H
   0.318    0.135    0.401 

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: 1021
Number of extensions: 23
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: 517
Length of database: 517
Length adjustment: 35
Effective length of query: 482
Effective length of database: 482
Effective search space:   232324
Effective search space used:   232324
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 GFF829 PS417_04210 (galactarate dehydrogenase)
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.20526.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   2.2e-293  959.2   0.0   2.4e-293  959.0   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF829  PS417_04210 galactarate dehydrog


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF829  PS417_04210 galactarate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  959.0   0.0  2.4e-293  2.4e-293       2     507 .]      12     517 .]      11     517 .] 1.00

  Alignments for each domain:
  == domain 1  score: 959.0 bits;  conditional E-value: 2.4e-293
                          TIGR03248   2 yirvneqdnvaivvndkGlpagtefedgltlvekipqghkvalvdlekgdaiirygeviGyavkdiarGswvkeel 77 
                                        +ir++e+dnv+ivvnd+G+pagtef+dgl++v+ ipq+hkv+l d+ +g +iiryg++iGya+  i+rGswv+e++
  lcl|FitnessBrowser__WCS417:GFF829  12 SIRLHERDNVVIVVNDQGVPAGTEFPDGLVTVDFIPQSHKVTLEDIPEGGQIIRYGQTIGYALAPIPRGSWVQEDQ 87 
                                        79************************************************************************** PP

                          TIGR03248  78 lelpsapaleelplatkvpeklapleGytfeGyrnadGsvGtknilgittsvqcvagvvdyavkrikkellpkypn 153
                                        l++p+ap+l++lpl+t+vpe++apleG+tfeGyrnadG+vGt+nilgitt+vqcv+gv+d+avkrik+ellpkyp 
  lcl|FitnessBrowser__WCS417:GFF829  88 LRMPTAPPLDSLPLSTEVPEAQAPLEGFTFEGYRNADGTVGTRNILGITTTVQCVTGVLDHAVKRIKDELLPKYPH 163
                                        **************************************************************************** PP

                          TIGR03248 154 vddvvalnhsyGcGvaidapdaivpirtlrnlalnpnlGGealvvglGceklqperllpeelsavelkdaavlrlq 229
                                        vddvval+hsyGcGvai+a+da++pirt+rnla+npnlGGealv++lGceklq+ ++++++ s+v+l++++++rlq
  lcl|FitnessBrowser__WCS417:GFF829 164 VDDVVALTHSYGCGVAITATDAYIPIRTVRNLARNPNLGGEALVISLGCEKLQAGQVMHDNDSSVDLSEPWLYRLQ 239
                                        **************************************************************************** PP

                          TIGR03248 230 deklGfaemveailelaeerlkklnarkretvpaselvvGlqcGGsdafsGvtanpavGfaadllvraGatvlfse 305
                                        d+++Gf+em+e+i++lae+rlkkl++r+retvpasel++G+qcGGsdafsG+tanpa+G+a+dll+raGatv+fse
  lcl|FitnessBrowser__WCS417:GFF829 240 DSSHGFTEMIEQIMALAETRLKKLDQRRRETVPASELILGMQCGGSDAFSGITANPALGYASDLLLRAGATVMFSE 315
                                        **************************************************************************** PP

                          TIGR03248 306 vtevrdaihlltpraedaevakaliremkwydeylarGeadrsanttpGnkkGGlsnivekalGsivksGssaive 381
                                        vtevrdai+llt+rae+++va+ l+rem+wyd+yla+GeadrsanttpGnkkGGlsnivek+lGsivksGssai++
  lcl|FitnessBrowser__WCS417:GFF829 316 VTEVRDAIYLLTSRAENTQVAQELVREMDWYDRYLAKGEADRSANTTPGNKKGGLSNIVEKSLGSIVKSGSSAING 391
                                        **************************************************************************** PP

                          TIGR03248 382 vlspGekvkkkGliyaatpasdfvcGtlqlasglnlhvfttGrGtpyGlalvpvikvstrtelaerwadlidldaG 457
                                        vl+pGe+ k kGli++atpasdfvcGtlqla+g+nlhvfttGrGtpyGla++pv+kvstrtela+rw dlid+daG
  lcl|FitnessBrowser__WCS417:GFF829 392 VLGPGERFKGKGLIFCATPASDFVCGTLQLAAGMNLHVFTTGRGTPYGLAMAPVVKVSTRTELAQRWPDLIDIDAG 467
                                        **************************************************************************** PP

                          TIGR03248 458 riatGeatiedvGwelfrlildvasGrkktwaekyklhndlalfnpapvt 507
                                        riatG+atie++Gwelf+++ldvasGrk+twae++klhnd++lfnpap+t
  lcl|FitnessBrowser__WCS417:GFF829 468 RIATGRATIEELGWELFHFYLDVASGRKQTWAEHHKLHNDITLFNPAPIT 517
                                        *************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (507 nodes)
Target sequences:                          1  (517 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: 00:00:00.03
# Mc/sec: 7.93
//
[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