Alignments for a candidate for pobA in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for pobA in Sinorhizobium meliloti 1021

Align p-hydroxybenzoate hydroxylase; PHBH; PHBHase; 4-hydroxybenzoate 3-monooxygenase; EC 1.14.13.2 (characterized)
to candidate SM_b20583 SM_b20583 4-hydroxybenzoate 3-monooxygenase

Query= SwissProt::P00438
         (394 letters)



>FitnessBrowser__Smeli:SM_b20583
          Length = 390

 Score =  523 bits (1347), Expect = e-153
 Identities = 249/390 (63%), Positives = 305/390 (78%)

Query: 1   MKTQVAIIGAGPSGLLLGQLLHKAGIDNVILERQTPDYVLGRIRAGVLEQGMVDLLREAG 60
           M+TQV IIG+GPSGLLLGQLL +AGI NVIL+R T  ++LGR+RAGVLEQG V L+ EAG
Sbjct: 1   MRTQVVIIGSGPSGLLLGQLLTEAGIANVILDRATKAHILGRVRAGVLEQGTVRLMEEAG 60

Query: 61  VDRRMARDGLVHEGVEIAFAGQRRRIDLKRLSGGKTVTVYGQTEVTRDLMEAREACGATT 120
              RM  +GL H+G  +AF G+  RIDL  L+GG+ V +YGQTE+TRDLM+ RE  GA +
Sbjct: 61  CGARMHAEGLPHDGFSLAFDGRDHRIDLFGLTGGRRVMIYGQTELTRDLMDHRERVGALS 120

Query: 121 VYQAAEVRLHDLQGERPYVTFERDGERLRLDCDYIAGCDGFHGISRQSIPAERLKVFERV 180
           +Y+AA V   D  G  P+V +E+DG   R+DCD+IAGCDGFHG+SR+S+P + ++ FE++
Sbjct: 121 IYEAANVMPRDFDGRTPHVAYEKDGIAQRIDCDFIAGCDGFHGVSRRSLPEKAIRNFEKI 180

Query: 181 YPFGWLGLLADTPPVSHELIYANHPRGFALCSQRSATRSRYYVQVPLTEKVEDWSDERFW 240
           YPFGWLG+LAD PPV HEL+YANHPRGFALCS RS TRSRYY+Q PL EK+EDW D+RFW
Sbjct: 181 YPFGWLGILADVPPVDHELVYANHPRGFALCSMRSHTRSRYYIQCPLEEKIEDWDDQRFW 240

Query: 241 TELKARLPAEVAEKLVTGPSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLN 300
            EL+ RLPA  AE++VTGPS EKSIAPLRSFV EPM+  RLFLAGDAAHIVPPTGAKGLN
Sbjct: 241 DELRRRLPAHHAERVVTGPSFEKSIAPLRSFVAEPMRFNRLFLAGDAAHIVPPTGAKGLN 300

Query: 301 LAASDVSTLYRLLLKAYREGRGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDTDAFS 360
           LAASDV  L+  LL+ Y++     ++ YSA  L R+WKA RFSWWMT++LHRFP+T  F 
Sbjct: 301 LAASDVHYLFEGLLEHYQDRSNAGIDAYSARALARVWKAVRFSWWMTTMLHRFPETSDFD 360

Query: 361 QRIQQTELEYYLGSEAGLATIAENYVGLPY 390
           QRIQ+ EL+Y   S A    +AENYVGLP+
Sbjct: 361 QRIQEAELDYLTHSRAAATALAENYVGLPF 390


Lambda     K      H
   0.321    0.138    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: 527
Number of extensions: 11
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: 390
Length adjustment: 31
Effective length of query: 363
Effective length of database: 359
Effective search space:   130317
Effective search space used:   130317
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 SM_b20583 SM_b20583 (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.6484.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   1.8e-209  681.3   0.0     2e-209  681.2   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SM_b20583  SM_b20583 4-hydroxybenzoate 3-mo


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SM_b20583  SM_b20583 4-hydroxybenzoate 3-monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  681.2   0.0    2e-209    2e-209       1     390 []       1     390 []       1     390 [] 1.00

  Alignments for each domain:
  == domain 1  score: 681.2 bits;  conditional E-value: 2e-209
                            TIGR02360   1 mktqvaiigaGpsGlllgqllhkaGidavilerksrdyvlgriraGvleqgtvdlleeagvderldreglvheG 74 
                                          m+tqv+iig+GpsGlllgqll +aGi++vil+r +++++lgr+raGvleqgtv l+eeag++ r+++egl+h+G
  lcl|FitnessBrowser__Smeli:SM_b20583   1 MRTQVVIIGSGPSGLLLGQLLTEAGIANVILDRATKAHILGRVRAGVLEQGTVRLMEEAGCGARMHAEGLPHDG 74 
                                          9************************************************************************* PP

                            TIGR02360  75 veiafegekvrvdlkkltggksvlvyGqtevtrdlyeareaaglktvyeadevrlhdlesdrpkvtfekdgeek 148
                                          + +af+g+ +r+dl  ltgg+ v++yGqte+trdl++ re++g+ ++yea++v + d+++ +p+v++ekdg  +
  lcl|FitnessBrowser__Smeli:SM_b20583  75 FSLAFDGRDHRIDLFGLTGGRRVMIYGQTELTRDLMDHRERVGALSIYEAANVMPRDFDGRTPHVAYEKDGIAQ 148
                                          ************************************************************************** PP

                            TIGR02360 149 rldcdfiaGcdGfhGvsrksipaeklkefekvypfGwlGilsetppvsdeliysnserGfalcslrsetrsryy 222
                                          r+dcdfiaGcdGfhGvsr+s+p++++++fek+ypfGwlGil+++ppv++el+y+n+ rGfalcs+rs+trsryy
  lcl|FitnessBrowser__Smeli:SM_b20583 149 RIDCDFIAGCDGFHGVSRRSLPEKAIRNFEKIYPFGWLGILADVPPVDHELVYANHPRGFALCSMRSHTRSRYY 222
                                          ************************************************************************** PP

                            TIGR02360 223 vqvsltdkvedwsddrfweelkrrldeeaaeklvtgpsieksiaplrsfvaepmryGrlflaGdaahivpptGa 296
                                          +q++l++k+edw d+rfw+el+rrl+ + ae++vtgps+eksiaplrsfvaepmr+ rlflaGdaahivpptGa
  lcl|FitnessBrowser__Smeli:SM_b20583 223 IQCPLEEKIEDWDDQRFWDELRRRLPAHHAERVVTGPSFEKSIAPLRSFVAEPMRFNRLFLAGDAAHIVPPTGA 296
                                          ************************************************************************** PP

                            TIGR02360 297 kGlnlaasdvaylyealleaykekdsaglerysakalarvwkaerfswwltsllhrfpdedefdkkiqqaeley 370
                                          kGlnlaasdv+yl+e+lle+y+++++ag+++ysa+alarvwka rfsww+t++lhrfp++++fd++iq+ael+y
  lcl|FitnessBrowser__Smeli:SM_b20583 297 KGLNLAASDVHYLFEGLLEHYQDRSNAGIDAYSARALARVWKAVRFSWWMTTMLHRFPETSDFDQRIQEAELDY 370
                                          ************************************************************************** PP

                            TIGR02360 371 lleseaaqktlaenyvGlpy 390
                                          l++s+aa ++laenyvGlp+
  lcl|FitnessBrowser__Smeli:SM_b20583 371 LTHSRAAATALAENYVGLPF 390
                                          *******************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (390 nodes)
Target sequences:                          1  (390 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: 00:00:00.01
# Mc/sec: 9.26
//
[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