GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuF in Paraburkholderia bryophila 376MFSha3.1

Align Maltose transport system permease protein malF aka TT_C1628, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized)
to candidate H281DRAFT_03746 H281DRAFT_03746 carbohydrate ABC transporter membrane protein 1, CUT1 family

Query= TCDB::Q72H67
         (291 letters)



>FitnessBrowser__Burk376:H281DRAFT_03746
          Length = 296

 Score =  189 bits (481), Expect = 5e-53
 Identities = 93/280 (33%), Positives = 164/280 (58%), Gaps = 3/280 (1%)

Query: 6   QVRLAWILVLPTLLVVVLVAGYPLAQVFYWSFFKADIAFVEPPEFVGLENYAYLFQDPDF 65
           +++  W+L+ P+L++ + +  YP+  + + S  +    F    +F GL+N+  +F DP F
Sbjct: 8   RLQAPWLLIAPSLVLALFIISYPIFNIVWQSLHEVS-RFGAIRDFTGLQNFYTIFGDPAF 66

Query: 66  RQALWNTLKFTVVSVSLETVLGLAIALIIHSNFRGRGLVRTAILIPWAIPTVVSAKMWQW 125
             A   T+ +TV  V    ++ + +AL+++ +F GRG+ RT +++PW++   ++A +W+W
Sbjct: 67  LAAARRTIVWTVFVVGGTVLISVPVALVLNQDFYGRGVARTIVMLPWSVSLTMTAVVWRW 126

Query: 126 MLNDVYGVINVLGVKLGLLSQKVAFLARPELLLPSIIAVDVWKTTPFMALLLLAGLQMIP 185
             ND YG++NV   +LGL+   + +LA PE   P  IAV +  + PF   +LL GL  +P
Sbjct: 127 AFNDDYGMVNVTLQRLGLIGGPIHWLATPEFAFPVEIAVGILVSIPFTVTILLGGLSSVP 186

Query: 186 EELYEAASIDGASRWQQFWSITLPLLTPALVVALIFRTLDALRVFDVVFVMS--GVNPAT 243
            ++YEAA IDGAS WQQF  +TLPLL P + + ++   +     F +++VM+  G + +T
Sbjct: 187 GDIYEAARIDGASAWQQFRKLTLPLLRPFINMTILLNVIYVFNSFPIIWVMTQGGPDNST 246

Query: 244 RTLAVYNRQTLVDFQDLGYGSAISVAILVIIFAFVLLYMR 283
             L  Y  +        G  +A+S+ +LV++F F + Y+R
Sbjct: 247 HILVTYLYELGFRLGRPGEAAAVSLIMLVMLFVFSMAYLR 286


Lambda     K      H
   0.329    0.142    0.433 

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: 268
Number of extensions: 16
Number of successful extensions: 3
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: 291
Length of database: 296
Length adjustment: 26
Effective length of query: 265
Effective length of database: 270
Effective search space:    71550
Effective search space used:    71550
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 bits)

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:

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