GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pobA in Rhizobium etli CFN 42

Align p-hydroxybenzoate hydroxylase; PHBH; PHBHase; 4-hydroxybenzoate 3-monooxygenase; EC 1.14.13.2 (characterized)
to candidate WP_042118977.1 RHE_RS17600 4-hydroxybenzoate 3-monooxygenase

Query= SwissProt::P00438
         (394 letters)



>NCBI__GCF_000092045.1:WP_042118977.1
          Length = 389

 Score =  524 bits (1349), Expect = e-153
 Identities = 254/390 (65%), Positives = 307/390 (78%), Gaps = 1/390 (0%)

Query: 1   MKTQVAIIGAGPSGLLLGQLLHKAGIDNVILERQTPDYVLGRIRAGVLEQGMVDLLREAG 60
           M+TQVAIIG+GPSGLLLGQLL +AG+DNVIL+R + +Y+LGR+RAGVLE+G V LL EA 
Sbjct: 1   MRTQVAIIGSGPSGLLLGQLLTEAGVDNVILDRVSKNYILGRVRAGVLEEGTVGLLDEAK 60

Query: 61  VDRRMARDGLVHEGVEIAFAGQRRRIDLKRLSGGKTVTVYGQTEVTRDLMEAREACGATT 120
              R+  +GL H+G  +AF G+  RIDL  L+G + VTVYGQTEVTRDLM+ REACG+ +
Sbjct: 61  AGARLHAEGLPHDGFSLAFDGRDHRIDLHELTG-RRVTVYGQTEVTRDLMQRREACGSLS 119

Query: 121 VYQAAEVRLHDLQGERPYVTFERDGERLRLDCDYIAGCDGFHGISRQSIPAERLKVFERV 180
           +Y AA+V  HD+ G  P+VT+ +DG   R+DCD+IAGCDGFHG SR+++P   ++ FE+V
Sbjct: 120 IYDAADVAPHDVDGGSPFVTYTKDGIGHRIDCDFIAGCDGFHGTSRRALPEGAVRSFEKV 179

Query: 181 YPFGWLGLLADTPPVSHELIYANHPRGFALCSQRSATRSRYYVQVPLTEKVEDWSDERFW 240
           YPFGWLGLLAD  PVS+ELIYANHPRGFALCS RSATRSRYY+Q PL  K+EDWSD+RFW
Sbjct: 180 YPFGWLGLLADVAPVSNELIYANHPRGFALCSMRSATRSRYYIQCPLDAKIEDWSDDRFW 239

Query: 241 TELKARLPAEVAEKLVTGPSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLN 300
            EL+ RLPA  AE L T PS EKSIAPLRSFV EPM+ GRLFL GDAAHIVPPTGAKGLN
Sbjct: 240 DELRRRLPAHHAEALTTAPSFEKSIAPLRSFVTEPMRFGRLFLVGDAAHIVPPTGAKGLN 299

Query: 301 LAASDVSTLYRLLLKAYREGRGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDTDAFS 360
           LAASDV  L+  LL+ YREG    ++ YS   L R+WKA RFSWWMT+++HRFPDT  F 
Sbjct: 300 LAASDVHYLFGGLLEHYREGSDSGIDAYSQTALTRVWKAVRFSWWMTTMMHRFPDTSDFD 359

Query: 361 QRIQQTELEYYLGSEAGLATIAENYVGLPY 390
           Q+IQ+ EL+Y   S A    +AENYVGLP+
Sbjct: 360 QKIQEAELDYLTHSRAASMVLAENYVGLPF 389


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: 522
Number of extensions: 14
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: 394
Length of database: 389
Length adjustment: 31
Effective length of query: 363
Effective length of database: 358
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 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate WP_042118977.1 RHE_RS17600 (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.522862.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.2e-206  669.1   0.0     1e-205  668.9   0.0    1.0  1  NCBI__GCF_000092045.1:WP_042118977.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000092045.1:WP_042118977.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  668.9   0.0    1e-205    1e-205       1     390 []       1     389 []       1     389 [] 1.00

  Alignments for each domain:
  == domain 1  score: 668.9 bits;  conditional E-value: 1e-205
                             TIGR02360   1 mktqvaiigaGpsGlllgqllhkaGidavilerksrdyvlgriraGvleqgtvdlleeagvderldreglvhe 73 
                                           m+tqvaiig+GpsGlllgqll +aG+d+vil+r s++y+lgr+raGvle+gtv ll+ea+++ rl++egl+h+
  NCBI__GCF_000092045.1:WP_042118977.1   1 MRTQVAIIGSGPSGLLLGQLLTEAGVDNVILDRVSKNYILGRVRAGVLEEGTVGLLDEAKAGARLHAEGLPHD 73 
                                           9************************************************************************ PP

                             TIGR02360  74 GveiafegekvrvdlkkltggksvlvyGqtevtrdlyeareaaglktvyeadevrlhdlesdrpkvtfekdge 146
                                           G+ +af+g+ +r+dl++ltg + v+vyGqtevtrdl++ rea+g+ ++y+a++v +hd+++ +p vt++kdg 
  NCBI__GCF_000092045.1:WP_042118977.1  74 GFSLAFDGRDHRIDLHELTG-RRVTVYGQTEVTRDLMQRREACGSLSIYDAADVAPHDVDGGSPFVTYTKDGI 145
                                           *******************9.**************************************************** PP

                             TIGR02360 147 ekrldcdfiaGcdGfhGvsrksipaeklkefekvypfGwlGilsetppvsdeliysnserGfalcslrsetrs 219
                                            +r+dcdfiaGcdGfhG sr+++p+ ++++fekvypfGwlG+l+++ pvs+eliy+n+ rGfalcs+rs+trs
  NCBI__GCF_000092045.1:WP_042118977.1 146 GHRIDCDFIAGCDGFHGTSRRALPEGAVRSFEKVYPFGWLGLLADVAPVSNELIYANHPRGFALCSMRSATRS 218
                                           ************************************************************************* PP

                             TIGR02360 220 ryyvqvsltdkvedwsddrfweelkrrldeeaaeklvtgpsieksiaplrsfvaepmryGrlflaGdaahivp 292
                                           ryy+q++l+ k+edwsddrfw+el+rrl+ + ae l t+ps+eksiaplrsfv+epmr+Grlfl+Gdaahivp
  NCBI__GCF_000092045.1:WP_042118977.1 219 RYYIQCPLDAKIEDWSDDRFWDELRRRLPAHHAEALTTAPSFEKSIAPLRSFVTEPMRFGRLFLVGDAAHIVP 291
                                           ************************************************************************* PP

                             TIGR02360 293 ptGakGlnlaasdvaylyealleaykekdsaglerysakalarvwkaerfswwltsllhrfpdedefdkkiqq 365
                                           ptGakGlnlaasdv+yl+ +lle+y+e++++g+++ys+ al+rvwka rfsww+t+++hrfpd+++fd+kiq+
  NCBI__GCF_000092045.1:WP_042118977.1 292 PTGAKGLNLAASDVHYLFGGLLEHYREGSDSGIDAYSQTALTRVWKAVRFSWWMTTMMHRFPDTSDFDQKIQE 364
                                           ************************************************************************* PP

                             TIGR02360 366 aeleylleseaaqktlaenyvGlpy 390
                                           ael+yl++s+aa  +laenyvGlp+
  NCBI__GCF_000092045.1:WP_042118977.1 365 AELDYLTHSRAASMVLAENYVGLPF 389
                                           ************************8 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 31.12
//
[ok]

This GapMind analysis is from Apr 09 2024. 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:

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:

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:

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:

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