Alignments for a candidate for pobA in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for pobA in Caulobacter crescentus NA1000

Align p-hydroxybenzoate hydroxylase; PHBH; 4-hydroxybenzoate 3-monooxygenase; EC 1.14.13.2 (characterized)
to candidate CCNA_02487 CCNA_02487 4-hydroxybenzoate 3-monooxygenase

Query= SwissProt::P20586
         (394 letters)



>FitnessBrowser__Caulo:CCNA_02487
          Length = 406

 Score =  491 bits (1263), Expect = e-143
 Identities = 238/389 (61%), Positives = 290/389 (74%)

Query: 1   MKTQVAIIGAGPSGLLLGQLLHKAGIDNVILERQTPDYVLGRIRAGVLEQGMVDLLREAG 60
           ++TQVAI+GAGP+GL LG LL +AG+D VILER+   YV GR+RAGVLE+  V+L+   G
Sbjct: 16  VRTQVAIVGAGPAGLFLGHLLRQAGVDVVILERKDRAYVEGRVRAGVLERITVELMERLG 75

Query: 61  VDRRMARDGLVHEGVEIAFAGQRRRIDLKRLSGGKTVTVYGQTEVTRDLMEAREACGATT 120
           VD RM R+GLVH G  +A  G+  RID+  L+GG TV VYGQ EV +DL +A E      
Sbjct: 76  VDERMRREGLVHAGANLASDGEMFRIDMAELTGGSTVMVYGQQEVMKDLFDAAEQRDLRI 135

Query: 121 VYQAAEVRLHDLQGERPYVTFERDGERLRLDCDYIAGCDGFHGISRQSIPAERLKVFERV 180
           V+ A  VRLHD++GERP++T+ +DG   RLDCD+IAGCDG+HG+SR +IP + LK FERV
Sbjct: 136 VFDADAVRLHDVEGERPHITWRKDGAEHRLDCDFIAGCDGYHGVSRATIPDKVLKTFERV 195

Query: 181 YPFGWLGLLADTPPVSHELIYANHPRGFALCSQRSATRSRYYVQVPLSEKVEDWSDERFW 240
           YPFGWLG+LA+ PP  HELIY+NH RGFAL S RS TRSRYYVQ  L +++EDWSDERFW
Sbjct: 196 YPFGWLGILAEAPPCDHELIYSNHDRGFALASMRSPTRSRYYVQCSLDDRLEDWSDERFW 255

Query: 241 TELKARLPSEVAEKLVTGPSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLN 300
            E+  RL  E A ++V  PS EKSIAPLRSFV EPM++GRLFLAGDAAHIVPPTGAKG+N
Sbjct: 256 DEVSVRLGPEAAARIVRAPSFEKSIAPLRSFVSEPMRYGRLFLAGDAAHIVPPTGAKGMN 315

Query: 301 LAASDVSTLYRLLLKAYREGRGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDTDAFS 360
           LA SDV  L   L++ Y E     ++ YSA  L R+WKAERFSWW TS+ HRFPD D F 
Sbjct: 316 LAVSDVIMLSEALVEHYHERSSAGIDGYSARALARVWKAERFSWWFTSLTHRFPDQDGFD 375

Query: 361 QRIQQTELEYYLGSEAGLATIAENYVGLP 389
           +++Q  EL Y  GS A   T+AENYVGLP
Sbjct: 376 RKMQVAELAYIKGSRAAQVTLAENYVGLP 404


Lambda     K      H
   0.321    0.138    0.413 

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: 502
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: 394
Length of database: 406
Length adjustment: 31
Effective length of query: 363
Effective length of database: 375
Effective search space:   136125
Effective search space used:   136125
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 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate CCNA_02487 CCNA_02487 (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.5156.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-219  714.9   0.0   1.3e-219  714.7   0.0    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_02487  CCNA_02487 4-hydroxybenzoate 3-m


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_02487  CCNA_02487 4-hydroxybenzoate 3-monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  714.7   0.0  1.3e-219  1.3e-219       2     390 .]      17     405 ..      16     405 .. 1.00

  Alignments for each domain:
  == domain 1  score: 714.7 bits;  conditional E-value: 1.3e-219
                             TIGR02360   2 ktqvaiigaGpsGlllgqllhkaGidavilerksrdyvlgriraGvleqgtvdlleeagvderldreglvheG 74 
                                           +tqvai+gaGp+Gl+lg+ll++aG+d+vilerk+r+yv+gr+raGvle++tv+l+e++gvder++reglvh+G
  lcl|FitnessBrowser__Caulo:CCNA_02487  17 RTQVAIVGAGPAGLFLGHLLRQAGVDVVILERKDRAYVEGRVRAGVLERITVELMERLGVDERMRREGLVHAG 89 
                                           9************************************************************************ PP

                             TIGR02360  75 veiafegekvrvdlkkltggksvlvyGqtevtrdlyeareaaglktvyeadevrlhdlesdrpkvtfekdgee 147
                                           +++a++ge++r+d+++ltgg++v+vyGq+ev++dl++a+e+++l++v++ad+vrlhd+e++rp++t++kdg+e
  lcl|FitnessBrowser__Caulo:CCNA_02487  90 ANLASDGEMFRIDMAELTGGSTVMVYGQQEVMKDLFDAAEQRDLRIVFDADAVRLHDVEGERPHITWRKDGAE 162
                                           ************************************************************************* PP

                             TIGR02360 148 krldcdfiaGcdGfhGvsrksipaeklkefekvypfGwlGilsetppvsdeliysnserGfalcslrsetrsr 220
                                           +rldcdfiaGcdG+hGvsr++ip+++lk+fe+vypfGwlGil+e+pp+++eliysn++rGfal+s+rs trsr
  lcl|FitnessBrowser__Caulo:CCNA_02487 163 HRLDCDFIAGCDGYHGVSRATIPDKVLKTFERVYPFGWLGILAEAPPCDHELIYSNHDRGFALASMRSPTRSR 235
                                           ************************************************************************* PP

                             TIGR02360 221 yyvqvsltdkvedwsddrfweelkrrldeeaaeklvtgpsieksiaplrsfvaepmryGrlflaGdaahivpp 293
                                           yyvq+sl+d++edwsd+rfw+e++ rl +eaa+++v++ps+eksiaplrsfv+epmryGrlflaGdaahivpp
  lcl|FitnessBrowser__Caulo:CCNA_02487 236 YYVQCSLDDRLEDWSDERFWDEVSVRLGPEAAARIVRAPSFEKSIAPLRSFVSEPMRYGRLFLAGDAAHIVPP 308
                                           ************************************************************************* PP

                             TIGR02360 294 tGakGlnlaasdvaylyealleaykekdsaglerysakalarvwkaerfswwltsllhrfpdedefdkkiqqa 366
                                           tGakG+nla+sdv++l+eal+e+y+e++sag+++ysa+alarvwkaerfsww+tsl+hrfpd+d fd+k+q+a
  lcl|FitnessBrowser__Caulo:CCNA_02487 309 TGAKGMNLAVSDVIMLSEALVEHYHERSSAGIDGYSARALARVWKAERFSWWFTSLTHRFPDQDGFDRKMQVA 381
                                           ************************************************************************* PP

                             TIGR02360 367 eleylleseaaqktlaenyvGlpy 390
                                           el+y+++s+aaq tlaenyvGlp+
  lcl|FitnessBrowser__Caulo:CCNA_02487 382 ELAYIKGSRAAQVTLAENYVGLPL 405
                                           **********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (390 nodes)
Target sequences:                          1  (406 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 11.38
//
[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