Alignments for a candidate for pobA in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for pobA in Acidovorax sp. GW101-3H11

Align 4-hydroxybenzoate 3-monooxygenase (EC 1.14.13.2) (characterized)
to candidate Ac3H11_3993 P-hydroxybenzoate hydroxylase (EC 1.14.13.2)

Query= reanno::Cup4G11:RR42_RS21940
         (389 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3993
          Length = 394

 Score =  536 bits (1381), Expect = e-157
 Identities = 266/389 (68%), Positives = 307/389 (78%), Gaps = 1/389 (0%)

Query: 1   MRTQVAIIGAGPAGLLLGQLLAKAGIDAVIVEQRSPDYILGRIRAGILESVTADALERAG 60
           MRTQVAIIGAGPAGLLLGQLL K+GIDAVI+EQRSPDY+LGRIRAG+LE V+ D L++AG
Sbjct: 1   MRTQVAIIGAGPAGLLLGQLLYKSGIDAVIIEQRSPDYVLGRIRAGVLEQVSMDLLDKAG 60

Query: 61  VAQRLQHDGLVHHGIELSYGGERHRIDFHALIGRS-VTVYGQTEVTRDLMAARQAGNAVT 119
           V  R   +GL H GIEL + G RHRID H L G S VTVYGQTEVTRDLM AR A    T
Sbjct: 61  VGARAHAEGLPHDGIELLFKGARHRIDLHDLTGGSRVTVYGQTEVTRDLMDARAAEGLTT 120

Query: 120 IYDAQDVSVHDFDTATPMVRYRKGGQQYELRCDFIAGCDGFHGVTRRSVPEPSRRIFERV 179
           +YDAQ+V VHDFD  +P V Y+K GQ +EL CDFIAGCDG+HGV R S P    + +ERV
Sbjct: 121 VYDAQNVQVHDFDGQSPRVTYQKDGQTHELACDFIAGCDGYHGVCRASAPADLLKTYERV 180

Query: 180 YPFGWLGVLADTPPVANELIYASHERGFALCSMRSLTRSRYYVQVSADERVEDWSDQRFW 239
           YPFGWLGVLAD PPV++ELIYA+ ERGFALCSMRS TRSRYYVQV + +++++W+  +FW
Sbjct: 181 YPFGWLGVLADVPPVSHELIYANTERGFALCSMRSATRSRYYVQVPSTDKIDNWTIDQFW 240

Query: 240 DELRSRLDTSAAEALVTGASIEKSIAPLRSFVCEPMRFGNLFLAGDAAHIVPPTGAKGLN 299
            EL +RLD  A   LVTG ++E SIAPLRSFV EPMRFG +FLAGDAAHIVPPTGAKGLN
Sbjct: 241 AELGNRLDPEARANLVTGPALEMSIAPLRSFVAEPMRFGRMFLAGDAAHIVPPTGAKGLN 300

Query: 300 LAASDVLYLADGLIARYLRDDASELDAYSQKCLRRVWKAERFSWWMTSLLHRFPDADDFA 359
           LAASDV YL   L   Y    A  +D YS +CLRRVW+AERFSWW TSL+HRFP+  +F 
Sbjct: 301 LAASDVGYLWTALTEFYTEKSAVGIDTYSDRCLRRVWRAERFSWWFTSLMHRFPETGEFG 360

Query: 360 LRIQQAELDYLAGSRAAQMSLAENYVGLP 388
            +IQ+AELDYL  SRAA +SLAENYVGLP
Sbjct: 361 QKIQEAELDYLVNSRAASVSLAENYVGLP 389


Lambda     K      H
   0.323    0.137    0.414 

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: 485
Number of extensions: 15
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: 389
Length of database: 394
Length adjustment: 31
Effective length of query: 358
Effective length of database: 363
Effective search space:   129954
Effective search space used:   129954
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 Ac3H11_3993 (P-hydroxybenzoate hydroxylase (EC 1.14.13.2))
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.20009.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   2.2e-207  674.5   0.0   2.5e-207  674.3   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3993  P-hydroxybenzoate hydroxylase (E


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3993  P-hydroxybenzoate hydroxylase (EC 1.14.13.2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  674.3   0.0  2.5e-207  2.5e-207       1     390 []       1     390 [.       1     390 [. 1.00

  Alignments for each domain:
  == domain 1  score: 674.3 bits;  conditional E-value: 2.5e-207
                                        TIGR02360   1 mktqvaiigaGpsGlllgqllhkaGidavilerksrdyvlgriraGvleqgtvdlleeagvd 62 
                                                      m+tqvaiigaGp+Glllgqll+k Gidavi+e++s+dyvlgriraGvleq+++dll++agv+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3993   1 MRTQVAIIGAGPAGLLLGQLLYKSGIDAVIIEQRSPDYVLGRIRAGVLEQVSMDLLDKAGVG 62 
                                                      9************************************************************* PP

                                        TIGR02360  63 erldreglvheGveiafegekvrvdlkkltggksvlvyGqtevtrdlyeareaaglktvyea 124
                                                       r+++egl+h+G+e+ f+g ++r+dl++ltgg+ v+vyGqtevtrdl++ar a gl+tvy+a
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3993  63 ARAHAEGLPHDGIELLFKGARHRIDLHDLTGGSRVTVYGQTEVTRDLMDARAAEGLTTVYDA 124
                                                      ************************************************************** PP

                                        TIGR02360 125 devrlhdlesdrpkvtfekdgeekrldcdfiaGcdGfhGvsrksipaeklkefekvypfGwl 186
                                                      ++v++hd+++++p+vt++kdg++++l cdfiaGcdG+hGv+r+s pa+ lk++e+vypfGwl
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3993 125 QNVQVHDFDGQSPRVTYQKDGQTHELACDFIAGCDGYHGVCRASAPADLLKTYERVYPFGWL 186
                                                      ************************************************************** PP

                                        TIGR02360 187 GilsetppvsdeliysnserGfalcslrsetrsryyvqvsltdkvedwsddrfweelkrrld 248
                                                      G+l+++ppvs+eliy+n erGfalcs+rs+trsryyvqv+ tdk+++w+ d+fw+el +rld
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3993 187 GVLADVPPVSHELIYANTERGFALCSMRSATRSRYYVQVPSTDKIDNWTIDQFWAELGNRLD 248
                                                      ************************************************************** PP

                                        TIGR02360 249 eeaaeklvtgpsieksiaplrsfvaepmryGrlflaGdaahivpptGakGlnlaasdvayly 310
                                                      +ea ++lvtgp++e siaplrsfvaepmr+Gr+flaGdaahivpptGakGlnlaasdv yl+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3993 249 PEARANLVTGPALEMSIAPLRSFVAEPMRFGRMFLAGDAAHIVPPTGAKGLNLAASDVGYLW 310
                                                      ************************************************************** PP

                                        TIGR02360 311 ealleaykekdsaglerysakalarvwkaerfswwltsllhrfpdedefdkkiqqaeleyll 372
                                                      +al+e+y+ek++ g+++ys+++l+rvw+aerfsww+tsl+hrfp++ ef +kiq+ael+yl+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3993 311 TALTEFYTEKSAVGIDTYSDRCLRRVWRAERFSWWFTSLMHRFPETGEFGQKIQEAELDYLV 372
                                                      ************************************************************** PP

                                        TIGR02360 373 eseaaqktlaenyvGlpy 390
                                                      +s+aa  +laenyvGlp+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3993 373 NSRAASVSLAENYVGLPM 390
                                                      ****************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (390 nodes)
Target sequences:                          1  (394 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: 9.38
//
[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