GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pobA in Amantichitinum ursilacus IGB-41

Align 3-hydroxybenzoate 4-monooxygenase; 3-hydroxybenzoate 4-hydroxylase; M-hydroxybenzoate hydroxylase; EC 1.14.13.23 (characterized)
to candidate WP_053936853.1 WG78_RS05840 hypothetical protein

Query= SwissProt::Q6SSJ6
         (639 letters)



>NCBI__GCF_001294205.1:WP_053936853.1
          Length = 507

 Score =  117 bits (293), Expect = 1e-30
 Identities = 113/375 (30%), Positives = 155/375 (41%), Gaps = 43/375 (11%)

Query: 35  VLIVGCGPAGLTLAAQLAAFPDIRTCIVEQKEGPMELGQADGIACRTMEMFEAFEFADSI 94
           VLIVG GP GLTLA  L     +   I+E+        +A  +  RT+EM E    A   
Sbjct: 5   VLIVGAGPIGLTLAMALTR-QAVPVRIIEKNAVRSPYSKALIVWSRTLEMLEIEGIAQDF 63

Query: 95  LKEACWINDVTFWKPDPAQPG-RIARHGRVQDTEDGLSEFPHVILNQARVHDHYLERMRN 153
           +           W     +   R A  G   D   G      V+L Q+         + N
Sbjct: 64  VAAGIPARGAAVWAEGKQRVQLRFAEAGIATDYPAG------VLLAQSETE----RLLEN 113

Query: 154 SPSRLEPHYARRVLDVKIDHGAADYPVTVTLERCDAAHAGQIETVQARYVVGCDGARSNV 213
             + L  H  R V    I H +    ++ TL   D    G+IET QA ++  CDGA S V
Sbjct: 114 HLATLGVHVEREV--ELIQHHSTPDGISATLRHAD----GRIETAQAAWLAACDGAHSTV 167

Query: 214 RRAIGR-QLVGDSANQAWGVMDVLAVTDFPDVRYKVAIQSEQGNVLIIPREGGHLVRFYV 272
           R  +   +  GD+    W + DV   +D P     + + +  G ++ IP   G   RF V
Sbjct: 168 RHQLDTAEFAGDTLPTHWLLADVKLASDLPRDEVSMFL-AHDGLLIAIPFGDG---RFRV 223

Query: 273 EMDKLDADERVASRNITVEQLIATAQRVLHPYK---LDVKNVPWWSVYEIGQRICAKYDD 329
             D    D     R    E  +A  Q +L          ++  W S + I +R+  +Y  
Sbjct: 224 MGDIGQVD-----RASLPEPTLADIQHLLDTRSDTPAVAQDPAWISHFVINERMVREYR- 277

Query: 330 VADAVATPDSPLPRVFIAGDACHTHSPKAGQGMNFSMQDSFNLGWKLAAVLRKQCAPELL 389
                        RVF+ GDA H HSP  GQGMN  MQD+ NL WKLA          LL
Sbjct: 278 -----------YGRVFLLGDAAHIHSPAGGQGMNTGMQDAINLAWKLALHSHGLVGEALL 326

Query: 390 HTYSSERQVVAQQLI 404
            +YSSER  +A Q++
Sbjct: 327 DSYSSERSAIADQVL 341


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: 790
Number of extensions: 52
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 639
Length of database: 507
Length adjustment: 36
Effective length of query: 603
Effective length of database: 471
Effective search space:   284013
Effective search space used:   284013
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: 53 (25.0 bits)

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:

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