Alignments for a candidate for garD in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for garD in Pseudomonas fluorescens FW300-N2E3

Align Galactarate dehydratase (EC 4.2.1.42) (characterized)
to candidate AO353_05290 AO353_05290 galactarate dehydratase

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



>FitnessBrowser__pseudo3_N2E3:AO353_05290
          Length = 517

 Score =  998 bits (2581), Expect = 0.0
 Identities = 496/517 (95%), Positives = 506/517 (97%)

Query: 1   MQLIEHADSPRSIRLHERDNVVIVVNDQGVPAGTEFPDGLVTVDFIPQSHKVTLEDIPEG 60
           MQLIEH+DSPR IRLHERDNVVIVVNDQGVPAGTEFPDGLVTV+F+PQSHKVTLEDIPEG
Sbjct: 1   MQLIEHSDSPRYIRLHERDNVVIVVNDQGVPAGTEFPDGLVTVEFVPQSHKVTLEDIPEG 60

Query: 61  GQIIRYGQTIGYALAPIPRGSWVQEDQLRMPTAPPLDSLPLSTEVPEAQAPLEGFTFEGY 120
           GQ+IRYGQTIGYAL  IPRGSWV+EDQLRMPTAPPLDSLPLSTEVP AQAPLEGFTFEGY
Sbjct: 61  GQVIRYGQTIGYALQSIPRGSWVKEDQLRMPTAPPLDSLPLSTEVPAAQAPLEGFTFEGY 120

Query: 121 RNADGTVGTRNILGITTTVQCVTGVLDHAVKRIKDELLPKYPHVDDVVALTHSYGCGVAI 180
           RNADGTVGTRNILGITTTVQCVTGVLDHAVKRIKDELLPKYPHVDDV+ALTHSYGCGVAI
Sbjct: 121 RNADGTVGTRNILGITTTVQCVTGVLDHAVKRIKDELLPKYPHVDDVIALTHSYGCGVAI 180

Query: 181 TATDAYIPIRTVRNLARNPNLGGEALVISLGCEKLQAGQVMHDNDSSVDLSEPWLYRLQD 240
           TATDAYIPIRTVRNLARNPNLGGEALVISLGCEKLQAGQVMH+NDSSVDLSEPWLYRLQD
Sbjct: 181 TATDAYIPIRTVRNLARNPNLGGEALVISLGCEKLQAGQVMHENDSSVDLSEPWLYRLQD 240

Query: 241 SSHGFTEMIEQIMALAETRLKKLDQRRRETVPASELILGMQCGGSDAFSGITANPALGYA 300
           SSHGF EMIEQIMALAE RL+KLD RRRETVPASELILGMQCGGSDAFSGITANPALGYA
Sbjct: 241 SSHGFGEMIEQIMALAEVRLRKLDLRRRETVPASELILGMQCGGSDAFSGITANPALGYA 300

Query: 301 SDLLLRAGATVMFSEVTEVRDAIYLLTSRAENTQVAQELVREMDWYDRYLAKGEADRSAN 360
           SDLLLRAGATVMFSEVTEVRDAIYLLTSRAE  QVAQELVREMDWYDRYLAKGEADRSAN
Sbjct: 301 SDLLLRAGATVMFSEVTEVRDAIYLLTSRAETKQVAQELVREMDWYDRYLAKGEADRSAN 360

Query: 361 TTPGNKKGGLSNIVEKSLGSIVKSGSSAINGVLGPGERFKGKGLIFCATPASDFVCGTLQ 420
           TTPGNKKGGLSNIVEKSLGSIVKSG+SAINGVLGPGERFK KGLIFCATPASDFVCGTLQ
Sbjct: 361 TTPGNKKGGLSNIVEKSLGSIVKSGNSAINGVLGPGERFKRKGLIFCATPASDFVCGTLQ 420

Query: 421 LAAGMNLHVFTTGRGTPYGLAMAPVVKVSTRTELAQRWPDLIDIDAGRIATGRATIEELG 480
           LAAGMNLHVFTTGRGTPYGLAMAPVVKVSTRTELAQRWPDLIDIDAGRIATGRA+IEELG
Sbjct: 421 LAAGMNLHVFTTGRGTPYGLAMAPVVKVSTRTELAQRWPDLIDIDAGRIATGRASIEELG 480

Query: 481 WELFHFYLDVASGRKQTWAEHHKLHNDITLFNPAPIT 517
           WELFHFYLDVASGRKQTWAE HKLHNDITLFNPAPIT
Sbjct: 481 WELFHFYLDVASGRKQTWAEQHKLHNDITLFNPAPIT 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: 985
Number of extensions: 20
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 AO353_05290 AO353_05290 (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.23180.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   2.4e-292  955.7   0.0   2.7e-292  955.6   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05290  AO353_05290 galactarate dehydrat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_05290  AO353_05290 galactarate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  955.6   0.0  2.7e-292  2.7e-292       2     507 .]      12     517 .]      11     517 .] 1.00

  Alignments for each domain:
  == domain 1  score: 955.6 bits;  conditional E-value: 2.7e-292
                                     TIGR03248   2 yirvneqdnvaivvndkGlpagtefedgltlvekipqghkvalvdlekgdaiirygeviGyavkd 66 
                                                   yir++e+dnv+ivvnd+G+pagtef+dgl++ve +pq+hkv+l d+ +g ++iryg++iGya+++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05290  12 YIRLHERDNVVIVVNDQGVPAGTEFPDGLVTVEFVPQSHKVTLEDIPEGGQVIRYGQTIGYALQS 76 
                                                   9**************************************************************** PP

                                     TIGR03248  67 iarGswvkeellelpsapaleelplatkvpeklapleGytfeGyrnadGsvGtknilgittsvqc 131
                                                   i+rGswvke++l++p+ap+l++lpl+t+vp+++apleG+tfeGyrnadG+vGt+nilgitt+vqc
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05290  77 IPRGSWVKEDQLRMPTAPPLDSLPLSTEVPAAQAPLEGFTFEGYRNADGTVGTRNILGITTTVQC 141
                                                   ***************************************************************** PP

                                     TIGR03248 132 vagvvdyavkrikkellpkypnvddvvalnhsyGcGvaidapdaivpirtlrnlalnpnlGGeal 196
                                                   v+gv+d+avkrik+ellpkyp vddv+al+hsyGcGvai+a+da++pirt+rnla+npnlGGeal
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05290 142 VTGVLDHAVKRIKDELLPKYPHVDDVIALTHSYGCGVAITATDAYIPIRTVRNLARNPNLGGEAL 206
                                                   ***************************************************************** PP

                                     TIGR03248 197 vvglGceklqperllpeelsavelkdaavlrlqdeklGfaemveailelaeerlkklnarkretv 261
                                                   v++lGceklq+ ++++e+ s+v+l++++++rlqd+++Gf em+e+i++lae rl+kl+ r+retv
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05290 207 VISLGCEKLQAGQVMHENDSSVDLSEPWLYRLQDSSHGFGEMIEQIMALAEVRLRKLDLRRRETV 271
                                                   ***************************************************************** PP

                                     TIGR03248 262 paselvvGlqcGGsdafsGvtanpavGfaadllvraGatvlfsevtevrdaihlltpraedaeva 326
                                                   pasel++G+qcGGsdafsG+tanpa+G+a+dll+raGatv+fsevtevrdai+llt+rae+++va
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05290 272 PASELILGMQCGGSDAFSGITANPALGYASDLLLRAGATVMFSEVTEVRDAIYLLTSRAETKQVA 336
                                                   ***************************************************************** PP

                                     TIGR03248 327 kaliremkwydeylarGeadrsanttpGnkkGGlsnivekalGsivksGssaivevlspGekvkk 391
                                                   + l+rem+wyd+yla+GeadrsanttpGnkkGGlsnivek+lGsivksG sai++vl+pGe+ k+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05290 337 QELVREMDWYDRYLAKGEADRSANTTPGNKKGGLSNIVEKSLGSIVKSGNSAINGVLGPGERFKR 401
                                                   ***************************************************************** PP

                                     TIGR03248 392 kGliyaatpasdfvcGtlqlasglnlhvfttGrGtpyGlalvpvikvstrtelaerwadlidlda 456
                                                   kGli++atpasdfvcGtlqla+g+nlhvfttGrGtpyGla++pv+kvstrtela+rw dlid+da
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05290 402 KGLIFCATPASDFVCGTLQLAAGMNLHVFTTGRGTPYGLAMAPVVKVSTRTELAQRWPDLIDIDA 466
                                                   ***************************************************************** PP

                                     TIGR03248 457 GriatGeatiedvGwelfrlildvasGrkktwaekyklhndlalfnpapvt 507
                                                   GriatG+a+ie++Gwelf+++ldvasGrk+twae++klhnd++lfnpap+t
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05290 467 GRIATGRASIEELGWELFHFYLDVASGRKQTWAEQHKLHNDITLFNPAPIT 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: 8.54
//
[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