Alignments for a candidate for garD in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for garD in Pseudomonas stutzeri RCH2

Align Galactarate dehydratase (EC 4.2.1.42) (characterized)
to candidate GFF376 Psest_0377 galactarate dehydratase

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



>FitnessBrowser__psRCH2:GFF376
          Length = 521

 Score =  864 bits (2232), Expect = 0.0
 Identities = 425/517 (82%), Positives = 468/517 (90%)

Query: 1   MQLIEHADSPRSIRLHERDNVVIVVNDQGVPAGTEFPDGLVTVDFIPQSHKVTLEDIPEG 60
           +QLI H DSPR IRL+E DNV +VVND GVP G +F  GLVTV+ +PQSHKV L DI EG
Sbjct: 5   VQLIPHQDSPRCIRLNEADNVAVVVNDGGVPVGAQFEGGLVTVEAVPQSHKVALVDIGEG 64

Query: 61  GQIIRYGQTIGYALAPIPRGSWVQEDQLRMPTAPPLDSLPLSTEVPEAQAPLEGFTFEGY 120
             + RYGQ IGYAL PI  GSWV+E QL+MP+APPL+SLP +T VP+  APL+G+TFEG+
Sbjct: 65  EPVRRYGQIIGYALEPIRCGSWVKETQLKMPSAPPLESLPRATAVPDKLAPLDGYTFEGF 124

Query: 121 RNADGTVGTRNILGITTTVQCVTGVLDHAVKRIKDELLPKYPHVDDVVALTHSYGCGVAI 180
           RN+DGTVGTRNILGI+TTVQCVTGVL+HAVKRI+DELLPKYP+VDDVVALTHSYGCGVAI
Sbjct: 125 RNSDGTVGTRNILGISTTVQCVTGVLEHAVKRIRDELLPKYPNVDDVVALTHSYGCGVAI 184

Query: 181 TATDAYIPIRTVRNLARNPNLGGEALVISLGCEKLQAGQVMHDNDSSVDLSEPWLYRLQD 240
            A DAYIPIRTVRNLARNPNLGGEALVISLGCEKLQA QVMH+ D SVDL EPWLYRLQ+
Sbjct: 185 NARDAYIPIRTVRNLARNPNLGGEALVISLGCEKLQAEQVMHEGDPSVDLREPWLYRLQE 244

Query: 241 SSHGFTEMIEQIMALAETRLKKLDQRRRETVPASELILGMQCGGSDAFSGITANPALGYA 300
           S+ GF EMIEQIMALAETRLKKLDQRRRETVPASELILGMQCGGSDAFSGITANPALGYA
Sbjct: 245 SNSGFGEMIEQIMALAETRLKKLDQRRRETVPASELILGMQCGGSDAFSGITANPALGYA 304

Query: 301 SDLLLRAGATVMFSEVTEVRDAIYLLTSRAENTQVAQELVREMDWYDRYLAKGEADRSAN 360
           +DLL+RAGATVMFSE TEVRDA+Y+LT+RAE  +VA  L+ EMDWYDRYL +G ADRSAN
Sbjct: 305 ADLLVRAGATVMFSENTEVRDAVYMLTARAETPEVADALIAEMDWYDRYLERGAADRSAN 364

Query: 361 TTPGNKKGGLSNIVEKSLGSIVKSGSSAINGVLGPGERFKGKGLIFCATPASDFVCGTLQ 420
           TTPGNKKGGLSNIVEKSLGSIVKSGS AI+GV+GPG R   KGLIFCATPASDFVCGTLQ
Sbjct: 365 TTPGNKKGGLSNIVEKSLGSIVKSGSGAISGVVGPGGRVARKGLIFCATPASDFVCGTLQ 424

Query: 421 LAAGMNLHVFTTGRGTPYGLAMAPVVKVSTRTELAQRWPDLIDIDAGRIATGRATIEELG 480
           LAAGMNLHVFTTGRGTPYGLAMAPVVKV+TRTELA+RWPDLIDIDAGRIA+GRA+IEELG
Sbjct: 425 LAAGMNLHVFTTGRGTPYGLAMAPVVKVATRTELAERWPDLIDIDAGRIASGRASIEELG 484

Query: 481 WELFHFYLDVASGRKQTWAEHHKLHNDITLFNPAPIT 517
           WELFH+YLDVASGR++TWAE H+LHND+ LFNPAPIT
Sbjct: 485 WELFHYYLDVASGRRKTWAEQHRLHNDLVLFNPAPIT 521


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: 928
Number of extensions: 30
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: 521
Length adjustment: 35
Effective length of query: 482
Effective length of database: 486
Effective search space:   234252
Effective search space used:   234252
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 GFF376 Psest_0377 (galactarate dehydratase)
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.8625.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   8.8e-286  934.1   0.0   9.9e-286  933.9   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF376  Psest_0377 galactarate dehydrata


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF376  Psest_0377 galactarate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  933.9   0.0  9.9e-286  9.9e-286       2     507 .]      16     521 .]      15     521 .] 1.00

  Alignments for each domain:
  == domain 1  score: 933.9 bits;  conditional E-value: 9.9e-286
                          TIGR03248   2 yirvneqdnvaivvndkGlpagtefedgltlvekipqghkvalvdlekgdaiirygeviGyavkdiarGswvkeel 77 
                                         ir+ne dnva+vvnd G+p g++fe gl++ve +pq+hkvalvd+ +g+ ++ryg++iGya++ i  Gswvke++
  lcl|FitnessBrowser__psRCH2:GFF376  16 CIRLNEADNVAVVVNDGGVPVGAQFEGGLVTVEAVPQSHKVALVDIGEGEPVRRYGQIIGYALEPIRCGSWVKETQ 91 
                                        69************************************************************************** PP

                          TIGR03248  78 lelpsapaleelplatkvpeklapleGytfeGyrnadGsvGtknilgittsvqcvagvvdyavkrikkellpkypn 153
                                        l++psap+le+lp at+vp klapl+GytfeG+rn+dG+vGt+nilgi t+vqcv+gv+++avkri++ellpkypn
  lcl|FitnessBrowser__psRCH2:GFF376  92 LKMPSAPPLESLPRATAVPDKLAPLDGYTFEGFRNSDGTVGTRNILGISTTVQCVTGVLEHAVKRIRDELLPKYPN 167
                                        **************************************************************************** PP

                          TIGR03248 154 vddvvalnhsyGcGvaidapdaivpirtlrnlalnpnlGGealvvglGceklqperllpeelsavelkdaavlrlq 229
                                        vddvval+hsyGcGvai+a da++pirt+rnla+npnlGGealv++lGceklq+e++++e+  +v+l +++++rlq
  lcl|FitnessBrowser__psRCH2:GFF376 168 VDDVVALTHSYGCGVAINARDAYIPIRTVRNLARNPNLGGEALVISLGCEKLQAEQVMHEGDPSVDLREPWLYRLQ 243
                                        **************************************************************************** PP

                          TIGR03248 230 deklGfaemveailelaeerlkklnarkretvpaselvvGlqcGGsdafsGvtanpavGfaadllvraGatvlfse 305
                                        +++ Gf em+e+i++lae+rlkkl++r+retvpasel++G+qcGGsdafsG+tanpa+G+aadllvraGatv+fse
  lcl|FitnessBrowser__psRCH2:GFF376 244 ESNSGFGEMIEQIMALAETRLKKLDQRRRETVPASELILGMQCGGSDAFSGITANPALGYAADLLVRAGATVMFSE 319
                                        **************************************************************************** PP

                          TIGR03248 306 vtevrdaihlltpraedaevakaliremkwydeylarGeadrsanttpGnkkGGlsnivekalGsivksGssaive 381
                                        +tevrda+++lt+rae+ eva ali em+wyd+yl+rG adrsanttpGnkkGGlsnivek+lGsivksGs ai++
  lcl|FitnessBrowser__psRCH2:GFF376 320 NTEVRDAVYMLTARAETPEVADALIAEMDWYDRYLERGAADRSANTTPGNKKGGLSNIVEKSLGSIVKSGSGAISG 395
                                        **************************************************************************** PP

                          TIGR03248 382 vlspGekvkkkGliyaatpasdfvcGtlqlasglnlhvfttGrGtpyGlalvpvikvstrtelaerwadlidldaG 457
                                        v++pG +v +kGli++atpasdfvcGtlqla+g+nlhvfttGrGtpyGla++pv+kv+trtelaerw dlid+daG
  lcl|FitnessBrowser__psRCH2:GFF376 396 VVGPGGRVARKGLIFCATPASDFVCGTLQLAAGMNLHVFTTGRGTPYGLAMAPVVKVATRTELAERWPDLIDIDAG 471
                                        **************************************************************************** PP

                          TIGR03248 458 riatGeatiedvGwelfrlildvasGrkktwaekyklhndlalfnpapvt 507
                                        ria+G+a+ie++Gwelf+ +ldvasGr+ktwae+++lhndl lfnpap+t
  lcl|FitnessBrowser__psRCH2:GFF376 472 RIASGRASIEELGWELFHYYLDVASGRRKTWAEQHRLHNDLVLFNPAPIT 521
                                        *************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (507 nodes)
Target sequences:                          1  (521 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: 00:00:00.02
# Mc/sec: 9.96
//
[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