Alignments for a candidate for pobA in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for pobA in Pseudomonas simiae WCS417

Align 4-hydroxybenzoate 3-monooxygenase (EC 1.14.13.2) (characterized)
to candidate GFF1441 PS417_07330 4-hydroxybenzoate 3-monooxygenase

Query= reanno::pseudo6_N2E2:Pf6N2E2_2914
         (396 letters)



>FitnessBrowser__WCS417:GFF1441
          Length = 397

 Score =  660 bits (1703), Expect = 0.0
 Identities = 321/397 (80%), Positives = 359/397 (90%), Gaps = 1/397 (0%)

Query: 1   MKTLKTQVAIIGAGPSGLLLGQLLHNAGIDTVILERQTPEYVLSRIRAGVLEQGMVELLR 60
           MKTLKTQVAIIGAGPSGLLLGQLLH AGI+T+ILERQ+ +YV  RIRAGVLEQGMV+LLR
Sbjct: 1   MKTLKTQVAIIGAGPSGLLLGQLLHEAGIETLILERQSADYVQGRIRAGVLEQGMVDLLR 60

Query: 61  QAGVGQRMDAEGLPHDGFELVLNDRRVHIDLKGLTGGKNVMVYGQTEVTRDLMAAREAAG 120
           QAGV +RMD+EGL HDGFEL LND+  HIDLKGLTGG++VM+YGQTEVTRDLMAAR AAG
Sbjct: 61  QAGVSRRMDSEGLVHDGFELALNDQLTHIDLKGLTGGQSVMIYGQTEVTRDLMAARTAAG 120

Query: 121 ARTLYLASNAQPHDMQTQTPFVTFEHEGETWRLDCDYIAGCDGFHGVARQSIPAEKLKVF 180
           A TLY A N QPH +++  P++TFEH+GE +RL+CDYIAGCDG+HGVARQSIPAE LKVF
Sbjct: 121 ATTLYEARNVQPHGLKSDRPWLTFEHQGEAFRLECDYIAGCDGYHGVARQSIPAESLKVF 180

Query: 181 ERVYPFGWLGVLADTPPVHEELVYARHTRGFALCSMRSKTRTRYYLQVPAEEQVADWPDE 240
           ERVYPFGWLG+LADTPPVH ELVYA+H+RGFALCSMRS TR+RYYLQVP EE + +W D 
Sbjct: 181 ERVYPFGWLGILADTPPVHAELVYAKHSRGFALCSMRSPTRSRYYLQVPVEEPIDEWSDA 240

Query: 241 RFWGELKNRLPADLAAALVTGPSIEKSIAPLRSFVVEPMQYGRMFLVGDAAHIVPPTGAK 300
           RFW ELK RLP+ LA  LVTGPSIEKSIAPLRSFVVEPMQYGR+FL+GDAAHIVPPTGAK
Sbjct: 241 RFWDELKTRLPSHLAEQLVTGPSIEKSIAPLRSFVVEPMQYGRLFLLGDAAHIVPPTGAK 300

Query: 301 GLNLAASDVSTLFNILLKVYRDGRVELLEKYSAICLRRVWKAERFSWWMTSMLHRFDD-D 359
           GLNLAASDVSTL+ ILLKVY +GRV+LLE+YSAICLRRVWKAERFSWWMTSMLH+F + D
Sbjct: 301 GLNLAASDVSTLYRILLKVYGEGRVDLLERYSAICLRRVWKAERFSWWMTSMLHQFPEAD 360

Query: 360 AFNQRISEAELEYFVDSEAGRKTIAENYVGLPYEAIE 396
            F QRI+E+ELEYF+ SEAGRKTIAENYVGLPYEAIE
Sbjct: 361 GFTQRIAESELEYFIHSEAGRKTIAENYVGLPYEAIE 397


Lambda     K      H
   0.321    0.137    0.415 

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: 608
Number of extensions: 12
Number of successful extensions: 2
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: 396
Length of database: 397
Length adjustment: 31
Effective length of query: 365
Effective length of database: 366
Effective search space:   133590
Effective search space used:   133590
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate GFF1441 PS417_07330 (4-hydroxybenzoate 3-monooxygenase)
to HMM TIGR02360 (pobA: 4-hydroxybenzoate 3-monooxygenase (EC 1.14.13.2))

# 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/TIGR02360.hmm
# target sequence database:        /tmp/gapView.26441.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02360  [M=390]
Accession:   TIGR02360
Description: pbenz_hydroxyl: 4-hydroxybenzoate 3-monooxygenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
     7e-208  676.1   0.0   8.1e-208  675.9   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF1441  PS417_07330 4-hydroxybenzoate 3-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF1441  PS417_07330 4-hydroxybenzoate 3-monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  675.9   0.0  8.1e-208  8.1e-208       1     390 []       4     393 ..       4     393 .. 1.00

  Alignments for each domain:
  == domain 1  score: 675.9 bits;  conditional E-value: 8.1e-208
                           TIGR02360   1 mktqvaiigaGpsGlllgqllhkaGidavilerksrdyvlgriraGvleqgtvdlleeagvderldreglvheGv 75 
                                         +ktqvaiigaGpsGlllgqllh+aGi+++iler+s+dyv+griraGvleqg+vdll++agv++r+d eglvh+G+
  lcl|FitnessBrowser__WCS417:GFF1441   4 LKTQVAIIGAGPSGLLLGQLLHEAGIETLILERQSADYVQGRIRAGVLEQGMVDLLRQAGVSRRMDSEGLVHDGF 78 
                                         69************************************************************************* PP

                           TIGR02360  76 eiafegekvrvdlkkltggksvlvyGqtevtrdlyeareaaglktvyeadevrlhdlesdrpkvtfekdgeekrl 150
                                         e+a +++ +++dlk ltgg+sv++yGqtevtrdl+ ar aag++t+yea +v++h l+sdrp +tfe++ge  rl
  lcl|FitnessBrowser__WCS417:GFF1441  79 ELALNDQLTHIDLKGLTGGQSVMIYGQTEVTRDLMAARTAAGATTLYEARNVQPHGLKSDRPWLTFEHQGEAFRL 153
                                         *************************************************************************** PP

                           TIGR02360 151 dcdfiaGcdGfhGvsrksipaeklkefekvypfGwlGilsetppvsdeliysnserGfalcslrsetrsryyvqv 225
                                         +cd+iaGcdG+hGv+r+sipae lk+fe+vypfGwlGil++tppv+ el+y++++rGfalcs+rs trsryy+qv
  lcl|FitnessBrowser__WCS417:GFF1441 154 ECDYIAGCDGYHGVARQSIPAESLKVFERVYPFGWLGILADTPPVHAELVYAKHSRGFALCSMRSPTRSRYYLQV 228
                                         *************************************************************************** PP

                           TIGR02360 226 sltdkvedwsddrfweelkrrldeeaaeklvtgpsieksiaplrsfvaepmryGrlflaGdaahivpptGakGln 300
                                         ++++ +++wsd+rfw+elk+rl+++ ae+lvtgpsieksiaplrsfv+epm+yGrlfl GdaahivpptGakGln
  lcl|FitnessBrowser__WCS417:GFF1441 229 PVEEPIDEWSDARFWDELKTRLPSHLAEQLVTGPSIEKSIAPLRSFVVEPMQYGRLFLLGDAAHIVPPTGAKGLN 303
                                         *************************************************************************** PP

                           TIGR02360 301 laasdvaylyealleaykekdsaglerysakalarvwkaerfswwltsllhrfpdedefdkkiqqaeleyllese 375
                                         laasdv++ly+ ll+ y e++ + lerysa +l+rvwkaerfsww+ts+lh+fp+ d f ++i ++eley+ +se
  lcl|FitnessBrowser__WCS417:GFF1441 304 LAASDVSTLYRILLKVYGEGRVDLLERYSAICLRRVWKAERFSWWMTSMLHQFPEADGFTQRIAESELEYFIHSE 378
                                         *************************************************************************** PP

                           TIGR02360 376 aaqktlaenyvGlpy 390
                                         a++kt+aenyvGlpy
  lcl|FitnessBrowser__WCS417:GFF1441 379 AGRKTIAENYVGLPY 393
                                         **************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (390 nodes)
Target sequences:                          1  (397 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02
# Mc/sec: 7.74
//
[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