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 3-hydroxybenzoate 4-monooxygenase; 3-hydroxybenzoate 4-hydroxylase; M-hydroxybenzoate hydroxylase; EC 1.14.13.23 (characterized)
to candidate WP_086508584.1 BZY95_RS03400 phenol 2-monooxygenase

Query= SwissProt::Q6SSJ6
         (639 letters)



>NCBI__GCF_002151265.1:WP_086508584.1
          Length = 629

 Score =  619 bits (1596), Expect = 0.0
 Identities = 338/645 (52%), Positives = 422/645 (65%), Gaps = 28/645 (4%)

Query: 1   MQFHLNGFRPGNPLIAPASPLAPAHTEAVPSQVDVLIVGCGPAGLTLAAQLAAFPDIRTC 60
           MQ+ L+G+R G+P I P +         +P +VDVLIVG GPAGL LAAQL+ FP+I T 
Sbjct: 1   MQYFLDGYRSGDPRIQPLAEGRSDEQGPLPEEVDVLIVGSGPAGLLLAAQLSTFPNIVTR 60

Query: 61  IVEQKEGPMELGQADGIACRTMEMFEAFEFADSILKEACWINDVTFWKPDPAQPGRIARH 120
           +VE+ +GP+E+G+ADGIACRT+EMFEAF  A+ +  EA W+N+  FW P P    RI R 
Sbjct: 61  VVEKSDGPLEVGRADGIACRTVEMFEAFGLAERMTSEAYWVNETHFWGPAPGDKSRITRL 120

Query: 121 GRVQDTEDGLSEFPHVILNQARVHDHYLERMRNSPSRLEPHYARRVLDVKIDHGAADYPV 180
           GRV+D   GLSEFPHVI+NQAR+ D  LE MRNSPSRL   Y    L V++     D  V
Sbjct: 121 GRVRDVRYGLSEFPHVIVNQARLLDFLLEYMRNSPSRLRVDYRHETLKVEVPE-TPDERV 179

Query: 181 TVTLERCDAAHAGQIETVQARYVVGCDGARSNVRRAIGRQLVGDSANQAWGVMDVLAVTD 240
           TV L+  +       + V ARYVVGCDGA S VR +IGR   G   ++AWGVMDVLAVTD
Sbjct: 180 TVRLKTPEGE-----KIVLARYVVGCDGAHSVVRDSIGRVPQGHGEDKAWGVMDVLAVTD 234

Query: 241 FPDVRYKVAIQS-EQGNVLIIPREGGHLVRFYVEMDKLDADERVASRNITVEQLIATAQR 299
           FPD+R+K  IQS E GN+L+IPREGG++VR YV+M  +  D       +T E+++A AQ 
Sbjct: 235 FPDIRFKCTIQSAEAGNILLIPREGGYMVRLYVDMGNIAPDAW-----LTKEEVLAKAQA 289

Query: 300 VLHPYKLDVKNVPWWSVYEIGQRICAKYDDVADAVATPDSPLPRVFIAGDACHTHSPKAG 359
           VL PY  +VK   W+SVY +G R+  K+DDV D     +S  PRVFIAGDACHTH+ KAG
Sbjct: 290 VLAPYTFEVKETAWFSVYRVGHRVTDKFDDVND--NQRESRTPRVFIAGDACHTHTAKAG 347

Query: 360 QGMNFSMQDSFNLGWKLAAVLRKQCAPELLHTYSSERQVVAQQLIDFDREWAKMFSDPAK 419
           QGMN SMQD+FNLGWKL +VL  +    LLHTY+ ER V+A+ LI+ D  W++     A 
Sbjct: 348 QGMNVSMQDTFNLGWKLISVLEGRSPASLLHTYNDERHVIAENLIEMDTRWSR-----AI 402

Query: 420 EGGQGGVDPK-------EFQKYFEQHGRFTAGVGTHYAPSLLTGQASHQALASGFTVGMR 472
              Q   DP+       E Q+ F  +  FTAG  THY P+LLTG   H ALA+GF  G R
Sbjct: 403 GAAQDADDPEAVMKGLAEVQRQFVTNSEFTAGFATHYTPALLTGDDQHLALATGFPPGRR 462

Query: 473 FHSAPVVRVSDAKPLQLGHCGKADGRWRLYAFAGQNDLAQPESGLLALCRFLESDAASPL 532
           FHSA V+R+ DAK + LGH  +ADGRWRLYAFA   D   P S    L  FL SD ASP+
Sbjct: 463 FHSAEVIRLGDAKQIHLGHVHRADGRWRLYAFADMVDPRSPGSRFNRLMDFLASD-ASPI 521

Query: 533 RRFTPSGQDIDSIFDLRAIFPQAYTEVALETLPALLLPPKGQLGMIDYEKVFSPDLKNAG 592
           RRFTP G D D++FD+  I  Q++ EV    +  +L P KG LG+ DY+KV +P L    
Sbjct: 522 RRFTPKGADPDAVFDVHGIIQQSHLEVDWADMHDVLKPHKGPLGLQDYQKVHAPVL-GTD 580

Query: 593 QDIFELRGIDRQQGALVVVRPDQYVAQVLPLGDHAALSAYFESFM 637
           +DIF+ RGIDR  GALVVVRPDQYV+ VLPL    AL+ +F  FM
Sbjct: 581 RDIFDQRGIDRGAGALVVVRPDQYVSLVLPLDGFEALTEFFSRFM 625


Lambda     K      H
   0.321    0.137    0.419 

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: 1119
Number of extensions: 39
Number of successful extensions: 8
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: 639
Length of database: 629
Length adjustment: 38
Effective length of query: 601
Effective length of database: 591
Effective search space:   355191
Effective search space used:   355191
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: 54 (25.4 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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