Alignments for a candidate for garD in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Alignments for a candidate for garD in Pseudomonas fluorescens FW300-N2E2

Align Galactarate dehydratase (EC 4.2.1.42) (characterized)
to candidate Pf6N2E2_3296 D-galactarate dehydratase (EC 4.2.1.42)

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



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3296
          Length = 517

 Score =  998 bits (2579), Expect = 0.0
 Identities = 494/517 (95%), Positives = 507/517 (98%)

Query: 1   MQLIEHADSPRSIRLHERDNVVIVVNDQGVPAGTEFPDGLVTVDFIPQSHKVTLEDIPEG 60
           MQLIEHADSPR IRLHERDNVVIVVNDQGVPAGTEFPDGLVTVDF+PQSHKVTLEDIP+G
Sbjct: 1   MQLIEHADSPRYIRLHERDNVVIVVNDQGVPAGTEFPDGLVTVDFVPQSHKVTLEDIPQG 60

Query: 61  GQIIRYGQTIGYALAPIPRGSWVQEDQLRMPTAPPLDSLPLSTEVPEAQAPLEGFTFEGY 120
           G++IRYGQ IGYAL PIPRGSWV+EDQLRMPTAPPLDSLPLST+VP A APLEG+TFEGY
Sbjct: 61  GEVIRYGQVIGYALQPIPRGSWVKEDQLRMPTAPPLDSLPLSTDVPVADAPLEGYTFEGY 120

Query: 121 RNADGTVGTRNILGITTTVQCVTGVLDHAVKRIKDELLPKYPHVDDVVALTHSYGCGVAI 180
           RNADGTVGTRNILGITTTVQCVTGVLDHAVKRIKDELLPKYP+VDDVVALTHSYGCGVAI
Sbjct: 121 RNADGTVGTRNILGITTTVQCVTGVLDHAVKRIKDELLPKYPNVDDVVALTHSYGCGVAI 180

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

Query: 241 SSHGFTEMIEQIMALAETRLKKLDQRRRETVPASELILGMQCGGSDAFSGITANPALGYA 300
           SSHGFTEMIEQIM LAETRLKKLDQRRRETVPASELILGMQCGGSDAFSGITANPALGYA
Sbjct: 241 SSHGFTEMIEQIMELAETRLKKLDQRRRETVPASELILGMQCGGSDAFSGITANPALGYA 300

Query: 301 SDLLLRAGATVMFSEVTEVRDAIYLLTSRAENTQVAQELVREMDWYDRYLAKGEADRSAN 360
           SDLLLRAGATVMFSEVTEVRDAIYLLTSRA+  +VAQELVREMDWYDRYLAKGEADRSAN
Sbjct: 301 SDLLLRAGATVMFSEVTEVRDAIYLLTSRAQTQEVAQELVREMDWYDRYLAKGEADRSAN 360

Query: 361 TTPGNKKGGLSNIVEKSLGSIVKSGSSAINGVLGPGERFKGKGLIFCATPASDFVCGTLQ 420
           TTPGNKKGGLSNIVEKSLGSIVKSGSSAINGVLGPGERFK KGLIFCATPASDFVCGTLQ
Sbjct: 361 TTPGNKKGGLSNIVEKSLGSIVKSGSSAINGVLGPGERFKQKGLIFCATPASDFVCGTLQ 420

Query: 421 LAAGMNLHVFTTGRGTPYGLAMAPVVKVSTRTELAQRWPDLIDIDAGRIATGRATIEELG 480
           LAAGMNLHVFTTGRGTPYGLAMAPVVKVSTRTELAQRWPDLIDIDAGRIATGRATIEELG
Sbjct: 421 LAAGMNLHVFTTGRGTPYGLAMAPVVKVSTRTELAQRWPDLIDIDAGRIATGRATIEELG 480

Query: 481 WELFHFYLDVASGRKQTWAEHHKLHNDITLFNPAPIT 517
           WELFH+YLDVASG+KQTWAE HKLHNDITLFNPAPIT
Sbjct: 481 WELFHYYLDVASGKKQTWAERHKLHNDITLFNPAPIT 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: 996
Number of extensions: 18
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 Pf6N2E2_3296 (D-galactarate dehydratase (EC 4.2.1.42))
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.10845.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   1.8e-296  969.3   0.0     2e-296  969.2   0.0    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3296  D-galactarate dehydratase (EC 4.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3296  D-galactarate dehydratase (EC 4.2.1.42)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  969.2   0.0    2e-296    2e-296       2     507 .]      12     517 .]      11     517 .] 1.00

  Alignments for each domain:
  == domain 1  score: 969.2 bits;  conditional E-value: 2e-296
                                      TIGR03248   2 yirvneqdnvaivvndkGlpagtefedgltlvekipqghkvalvdlekgdaiirygeviGyavk 65 
                                                    yir++e+dnv+ivvnd+G+pagtef+dgl++v+ +pq+hkv+l d+ +g ++iryg+viGya++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3296  12 YIRLHERDNVVIVVNDQGVPAGTEFPDGLVTVDFVPQSHKVTLEDIPQGGEVIRYGQVIGYALQ 75 
                                                    9*************************************************************** PP

                                      TIGR03248  66 diarGswvkeellelpsapaleelplatkvpeklapleGytfeGyrnadGsvGtknilgittsv 129
                                                     i+rGswvke++l++p+ap+l++lpl+t vp++ apleGytfeGyrnadG+vGt+nilgitt+v
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3296  76 PIPRGSWVKEDQLRMPTAPPLDSLPLSTDVPVADAPLEGYTFEGYRNADGTVGTRNILGITTTV 139
                                                    **************************************************************** PP

                                      TIGR03248 130 qcvagvvdyavkrikkellpkypnvddvvalnhsyGcGvaidapdaivpirtlrnlalnpnlGG 193
                                                    qcv+gv+d+avkrik+ellpkypnvddvval+hsyGcGvai+a+da++pirt+rnla+npnlGG
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3296 140 QCVTGVLDHAVKRIKDELLPKYPNVDDVVALTHSYGCGVAITATDAYIPIRTVRNLARNPNLGG 203
                                                    **************************************************************** PP

                                      TIGR03248 194 ealvvglGceklqperllpeelsavelkdaavlrlqdeklGfaemveailelaeerlkklnark 257
                                                    ealv++lGceklq+ ++++e+ s+v+l++++++rlqd+++Gf+em+e+i+elae+rlkkl++r+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3296 204 EALVISLGCEKLQAGQVMHENDSSVDLSEPWLYRLQDSSHGFTEMIEQIMELAETRLKKLDQRR 267
                                                    **************************************************************** PP

                                      TIGR03248 258 retvpaselvvGlqcGGsdafsGvtanpavGfaadllvraGatvlfsevtevrdaihlltprae 321
                                                    retvpasel++G+qcGGsdafsG+tanpa+G+a+dll+raGatv+fsevtevrdai+llt+ra+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3296 268 RETVPASELILGMQCGGSDAFSGITANPALGYASDLLLRAGATVMFSEVTEVRDAIYLLTSRAQ 331
                                                    **************************************************************** PP

                                      TIGR03248 322 daevakaliremkwydeylarGeadrsanttpGnkkGGlsnivekalGsivksGssaivevlsp 385
                                                    ++eva+ l+rem+wyd+yla+GeadrsanttpGnkkGGlsnivek+lGsivksGssai++vl+p
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3296 332 TQEVAQELVREMDWYDRYLAKGEADRSANTTPGNKKGGLSNIVEKSLGSIVKSGSSAINGVLGP 395
                                                    **************************************************************** PP

                                      TIGR03248 386 GekvkkkGliyaatpasdfvcGtlqlasglnlhvfttGrGtpyGlalvpvikvstrtelaerwa 449
                                                    Ge+ k+kGli++atpasdfvcGtlqla+g+nlhvfttGrGtpyGla++pv+kvstrtela+rw 
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3296 396 GERFKQKGLIFCATPASDFVCGTLQLAAGMNLHVFTTGRGTPYGLAMAPVVKVSTRTELAQRWP 459
                                                    **************************************************************** PP

                                      TIGR03248 450 dlidldaGriatGeatiedvGwelfrlildvasGrkktwaekyklhndlalfnpapvt 507
                                                    dlid+daGriatG+atie++Gwelf+ +ldvasG+k+twae++klhnd++lfnpap+t
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3296 460 DLIDIDAGRIATGRATIEELGWELFHYYLDVASGKKQTWAERHKLHNDITLFNPAPIT 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: 00:00:00.02
# Mc/sec: 10.99
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
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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