Alignments for a candidate for pobA in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for pobA in Dinoroseobacter shibae DFL-12

Align 4-hydroxybenzoate 3-monooxygenase (EC 1.14.13.2) (characterized)
to candidate 3610098 Dshi_3479 4-hydroxybenzoate 3-monooxygenase (RefSeq)

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



>FitnessBrowser__Dino:3610098
          Length = 389

 Score =  487 bits (1254), Expect = e-142
 Identities = 235/389 (60%), Positives = 291/389 (74%)

Query: 1   MRTQVAIIGAGPAGLLLGQLLAKAGIDAVIVEQRSPDYILGRIRAGILESVTADALERAG 60
           MRTQVAIIG GP+GLLL QLL + GID V++E++S  ++LGRIRAG+LE    D +  AG
Sbjct: 1   MRTQVAIIGGGPSGLLLSQLLHRRGIDTVVLERQSRAHVLGRIRAGVLERGLVDLMIEAG 60

Query: 61  VAQRLQHDGLVHHGIELSYGGERHRIDFHALIGRSVTVYGQTEVTRDLMAARQAGNAVTI 120
           V  R+Q +G+ H G  +S+G E  RIDF AL G+ VTVYGQTEVTRDL  AR+A   + +
Sbjct: 61  VGDRVQREGIPHDGTVISHGDEMFRIDFTALTGQPVTVYGQTEVTRDLYTAREAAGGILL 120

Query: 121 YDAQDVSVHDFDTATPMVRYRKGGQQYELRCDFIAGCDGFHGVTRRSVPEPSRRIFERVY 180
           +  + V +   DT TP V Y   GQ+  L CDF+AGCDGFHG++R+++PE +RR FE+VY
Sbjct: 121 HGVEGVEIQGADTDTPSVSYTLDGQRQHLSCDFVAGCDGFHGISRKTIPETARREFEKVY 180

Query: 181 PFGWLGVLADTPPVANELIYASHERGFALCSMRSLTRSRYYVQVSADERVEDWSDQRFWD 240
           PFGWLGVL++TPPV  ELIYA+ ERGFALCSMR+   SRYY+Q   D+R EDWSD  FWD
Sbjct: 181 PFGWLGVLSETPPVHEELIYANSERGFALCSMRNANLSRYYIQCRLDDRPEDWSDSAFWD 240

Query: 241 ELRSRLDTSAAEALVTGASIEKSIAPLRSFVCEPMRFGNLFLAGDAAHIVPPTGAKGLNL 300
           ELR R+    AE+L+TG SIEKSIAPLRSFV EPMR+G LFL GDAAHIVPPTGAKGLN 
Sbjct: 241 ELRRRIPKPQAESLITGPSIEKSIAPLRSFVTEPMRWGRLFLCGDAAHIVPPTGAKGLNT 300

Query: 301 AASDVLYLADGLIARYLRDDASELDAYSQKCLRRVWKAERFSWWMTSLLHRFPDADDFAL 360
           AASDV YL +GL   Y   D+  ++ YS+K L RVWK ERFSWW + L+HRFPD  +F  
Sbjct: 301 AASDVHYLYNGLRQFYEDGDSEGINRYSEKALARVWKTERFSWWFSKLMHRFPDQSEFEH 360

Query: 361 RIQQAELDYLAGSRAAQMSLAENYVGLPY 389
           +IQ AE+D+L  + AAQ ++A+NYVGLPY
Sbjct: 361 KIQLAEIDFLRSNTAAQTAMAQNYVGLPY 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: 423
Number of extensions: 10
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: 389
Length of database: 389
Length adjustment: 30
Effective length of query: 359
Effective length of database: 359
Effective search space:   128881
Effective search space used:   128881
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 3610098 Dshi_3479 (4-hydroxybenzoate 3-monooxygenase (RefSeq))
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.3623.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.6e-208  678.1   0.0   1.8e-208  678.0   0.0    1.0  1  lcl|FitnessBrowser__Dino:3610098  Dshi_3479 4-hydroxybenzoate 3-mo


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3610098  Dshi_3479 4-hydroxybenzoate 3-monooxygenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  678.0   0.0  1.8e-208  1.8e-208       1     390 []       1     389 []       1     389 [] 1.00

  Alignments for each domain:
  == domain 1  score: 678.0 bits;  conditional E-value: 1.8e-208
                         TIGR02360   1 mktqvaiigaGpsGlllgqllhkaGidavilerksrdyvlgriraGvleqgtvdlleeagvderldreglvheGvei 77 
                                       m+tqvaiig+GpsGlll+qllh++Gid+v+ler+sr++vlgriraGvle+g vdl+ eagv++r++reg++h+G++i
  lcl|FitnessBrowser__Dino:3610098   1 MRTQVAIIGGGPSGLLLSQLLHRRGIDTVVLERQSRAHVLGRIRAGVLERGLVDLMIEAGVGDRVQREGIPHDGTVI 77 
                                       9**************************************************************************** PP

                         TIGR02360  78 afegekvrvdlkkltggksvlvyGqtevtrdlyeareaaglktvyeadevrlhdlesdrpkvtfekdgeekrldcdf 154
                                       ++ +e++r+d+++ltg + v+vyGqtevtrdly areaag+  ++ ++ v+++ +++d+p v+++ dg++++l cdf
  lcl|FitnessBrowser__Dino:3610098  78 SHGDEMFRIDFTALTG-QPVTVYGQTEVTRDLYTAREAAGGILLHGVEGVEIQGADTDTPSVSYTLDGQRQHLSCDF 153
                                       ***************9.************************************************************ PP

                         TIGR02360 155 iaGcdGfhGvsrksipaeklkefekvypfGwlGilsetppvsdeliysnserGfalcslrsetrsryyvqvsltdkv 231
                                       +aGcdGfhG+srk+ip+ +++efekvypfGwlG+lsetppv++eliy+nserGfalcs+r++++sryy+q+ l+d+ 
  lcl|FitnessBrowser__Dino:3610098 154 VAGCDGFHGISRKTIPETARREFEKVYPFGWLGVLSETPPVHEELIYANSERGFALCSMRNANLSRYYIQCRLDDRP 230
                                       ***************************************************************************** PP

                         TIGR02360 232 edwsddrfweelkrrldeeaaeklvtgpsieksiaplrsfvaepmryGrlflaGdaahivpptGakGlnlaasdvay 308
                                       edwsd +fw+el+rr+++  ae+l+tgpsieksiaplrsfv+epmr+Grlfl+GdaahivpptGakGln+aasdv+y
  lcl|FitnessBrowser__Dino:3610098 231 EDWSDSAFWDELRRRIPKPQAESLITGPSIEKSIAPLRSFVTEPMRWGRLFLCGDAAHIVPPTGAKGLNTAASDVHY 307
                                       ***************************************************************************** PP

                         TIGR02360 309 lyealleaykekdsaglerysakalarvwkaerfswwltsllhrfpdedefdkkiqqaeleylleseaaqktlaeny 385
                                       ly++l+++y+++ds+g++rys+kalarvwk+erfsww+++l+hrfpd++ef++kiq ae+++l++++aaq+++a+ny
  lcl|FitnessBrowser__Dino:3610098 308 LYNGLRQFYEDGDSEGINRYSEKALARVWKTERFSWWFSKLMHRFPDQSEFEHKIQLAEIDFLRSNTAAQTAMAQNY 384
                                       ***************************************************************************** PP

                         TIGR02360 386 vGlpy 390
                                       vGlpy
  lcl|FitnessBrowser__Dino:3610098 385 VGLPY 389
                                       ****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (390 nodes)
Target sequences:                          1  (389 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: 10.68
//
[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