Alignments for a candidate for pobA in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for pobA in Halomonas desiderata SP1

Align p-hydroxybenzoate hydroxylase; PHBH; 4-hydroxybenzoate 3-monooxygenase; EC 1.14.13.2 (characterized)
to candidate WP_086508579.1 BZY95_RS03375 4-hydroxybenzoate 3-monooxygenase

Query= SwissProt::P20586
         (394 letters)



>NCBI__GCF_002151265.1:WP_086508579.1
          Length = 394

 Score =  623 bits (1606), Expect = 0.0
 Identities = 303/394 (76%), Positives = 340/394 (86%)

Query: 1   MKTQVAIIGAGPSGLLLGQLLHKAGIDNVILERQTPDYVLGRIRAGVLEQGMVDLLREAG 60
           MKTQVAIIGAGPSGLLLGQLL + GIDNVILER++ +YVL RIRAGVLEQGMVDLLREAG
Sbjct: 1   MKTQVAIIGAGPSGLLLGQLLSRQGIDNVILERKSGEYVLSRIRAGVLEQGMVDLLREAG 60

Query: 61  VDRRMARDGLVHEGVEIAFAGQRRRIDLKRLSGGKTVTVYGQTEVTRDLMEAREACGATT 120
           VD RM  +GL H+GVE+AF  +R RIDL  L+GGKTV VYGQTEVTRDLMEAR A G TT
Sbjct: 61  VDARMNEEGLPHDGVELAFDNRRVRIDLAGLTGGKTVMVYGQTEVTRDLMEARAAGGGTT 120

Query: 121 VYQAAEVRLHDLQGERPYVTFERDGERLRLDCDYIAGCDGFHGISRQSIPAERLKVFERV 180
           +Y+A  V+ HDL+ + PYVTF +DGE +RLDCDY+AGCDGFHG+SRQSIP +R+K FE++
Sbjct: 121 IYEADNVQPHDLETDAPYVTFVKDGETVRLDCDYVAGCDGFHGVSRQSIPKDRIKEFEKI 180

Query: 181 YPFGWLGLLADTPPVSHELIYANHPRGFALCSQRSATRSRYYVQVPLSEKVEDWSDERFW 240
           YPFGWLGLLADTPPVS ELIYA H RGFALCS RS TRSRYYVQVPL EKVEDWSDERFW
Sbjct: 181 YPFGWLGLLADTPPVSDELIYARHERGFALCSMRSPTRSRYYVQVPLDEKVEDWSDERFW 240

Query: 241 TELKARLPSEVAEKLVTGPSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLN 300
            ELK RLP EVA KLVTGP+LEKSIAPLRSFVVEPMQ+GRLFL GDAAHIVPPTGAKGLN
Sbjct: 241 AELKRRLPEEVAAKLVTGPALEKSIAPLRSFVVEPMQYGRLFLVGDAAHIVPPTGAKGLN 300

Query: 301 LAASDVSTLYRLLLKAYREGRGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDTDAFS 360
           LAASDV+TLYRL++K Y+EGR +L+  YS  CL+RIWKAERFSWWMTS+LH+F D + F 
Sbjct: 301 LAASDVNTLYRLMVKVYQEGRTDLIPNYSQTCLKRIWKAERFSWWMTSLLHKFSDEEGFE 360

Query: 361 QRIQQTELEYYLGSEAGLATIAENYVGLPYEEIE 394
            R+QQ EL+Y   SEAGL TIAENYVGLPYE +E
Sbjct: 361 TRMQQAELDYLTSSEAGLKTIAENYVGLPYESLE 394


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: 585
Number of extensions: 12
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: 394
Length adjustment: 31
Effective length of query: 363
Effective length of database: 363
Effective search space:   131769
Effective search space used:   131769
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_086508579.1 BZY95_RS03375 (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.29540.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.3e-219  713.3   0.0   3.7e-219  713.2   0.0    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086508579.1  BZY95_RS03375 4-hydroxybenzoate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086508579.1  BZY95_RS03375 4-hydroxybenzoate 3-monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  713.2   0.0  3.7e-219  3.7e-219       1     390 []       1     390 [.       1     390 [. 1.00

  Alignments for each domain:
  == domain 1  score: 713.2 bits;  conditional E-value: 3.7e-219
                                 TIGR02360   1 mktqvaiigaGpsGlllgqllhkaGidavilerksrdyvlgriraGvleqgtvdlleeagvderldreg 69 
                                               mktqvaiigaGpsGlllgqll ++Gid+vilerks +yvl+riraGvleqg+vdll+eagvd r+++eg
  lcl|NCBI__GCF_002151265.1:WP_086508579.1   1 MKTQVAIIGAGPSGLLLGQLLSRQGIDNVILERKSGEYVLSRIRAGVLEQGMVDLLREAGVDARMNEEG 69 
                                               9******************************************************************** PP

                                 TIGR02360  70 lvheGveiafegekvrvdlkkltggksvlvyGqtevtrdlyeareaaglktvyeadevrlhdlesdrpk 138
                                               l+h+Gve+af++++vr+dl+ ltggk+v+vyGqtevtrdl+ear a g++t+yead+v++hdle+d+p+
  lcl|NCBI__GCF_002151265.1:WP_086508579.1  70 LPHDGVELAFDNRRVRIDLAGLTGGKTVMVYGQTEVTRDLMEARAAGGGTTIYEADNVQPHDLETDAPY 138
                                               ********************************************************************* PP

                                 TIGR02360 139 vtfekdgeekrldcdfiaGcdGfhGvsrksipaeklkefekvypfGwlGilsetppvsdeliysnserG 207
                                               vtf kdge++rldcd++aGcdGfhGvsr+sip++++kefek+ypfGwlG+l++tppvsdeliy+++erG
  lcl|NCBI__GCF_002151265.1:WP_086508579.1 139 VTFVKDGETVRLDCDYVAGCDGFHGVSRQSIPKDRIKEFEKIYPFGWLGLLADTPPVSDELIYARHERG 207
                                               ********************************************************************* PP

                                 TIGR02360 208 falcslrsetrsryyvqvsltdkvedwsddrfweelkrrldeeaaeklvtgpsieksiaplrsfvaepm 276
                                               falcs+rs trsryyvqv+l++kvedwsd+rfw+elkrrl+ee+a+klvtgp++eksiaplrsfv+epm
  lcl|NCBI__GCF_002151265.1:WP_086508579.1 208 FALCSMRSPTRSRYYVQVPLDEKVEDWSDERFWAELKRRLPEEVAAKLVTGPALEKSIAPLRSFVVEPM 276
                                               ********************************************************************* PP

                                 TIGR02360 277 ryGrlflaGdaahivpptGakGlnlaasdvaylyealleaykekdsaglerysakalarvwkaerfsww 345
                                               +yGrlfl+GdaahivpptGakGlnlaasdv++ly+ +++ y+e++++ + +ys+ +l+r+wkaerfsww
  lcl|NCBI__GCF_002151265.1:WP_086508579.1 277 QYGRLFLVGDAAHIVPPTGAKGLNLAASDVNTLYRLMVKVYQEGRTDLIPNYSQTCLKRIWKAERFSWW 345
                                               ********************************************************************* PP

                                 TIGR02360 346 ltsllhrfpdedefdkkiqqaeleylleseaaqktlaenyvGlpy 390
                                               +tsllh+f de+ f++++qqael+yl++sea++kt+aenyvGlpy
  lcl|NCBI__GCF_002151265.1:WP_086508579.1 346 MTSLLHKFSDEEGFETRMQQAELDYLTSSEAGLKTIAENYVGLPY 390
                                               ********************************************9 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: 11.57
//
[ok]

This GapMind analysis is from Sep 24 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