GapMind for catabolism of small carbon sources

 

Aligments for a candidate for thuF in Sinorhizobium meliloti 1021

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 SMa0710 SMa0710 ABC transporter permease

Query= TCDB::Q72H67
         (291 letters)



>lcl|FitnessBrowser__Smeli:SMa0710 SMa0710 ABC transporter permease
          Length = 337

 Score =  189 bits (479), Expect = 1e-52
 Identities = 101/281 (35%), Positives = 161/281 (57%), Gaps = 3/281 (1%)

Query: 5   RQVRLAWILVLPTLLVVVLVAGYPLAQVFYWSFFKADIAFVEPPEF-VGLENYAYLFQDP 63
           RQ  L ++L+LP + +V L+  YPL      SF K  +A +  P     LENY  LF  P
Sbjct: 49  RQHWLGYLLLLPAVALVALIIVYPLFVSLDLSFQKIGMATLSAPRKPFTLENYHKLFASP 108

Query: 64  DFRQALWNTLKFTVVSVSLETVLGLAIALIIHSNFRGRGLVRTAILIPWAIPTVVSAKMW 123
           DF  + W T+K  VV  +    +GL  AL++++ F+GR L R  + +PWA+P V++  ++
Sbjct: 109 DFWNSCWVTIKLVVVVSAACFAVGLGTALLVNNRFKGRTLARLFVALPWAVPEVIAVVIF 168

Query: 124 QWMLNDVYGVINVLGVKLGLLSQKVAFLARPELLLPSIIAVDVWKTTPFMALLLLAGLQM 183
            W+ +  +G++N L +KLG+ SQ + + + P      +    +WK  PF++++ LAGLQ 
Sbjct: 169 AWIFDSSFGLMNWLFIKLGITSQMINWFSEPTAAFWVVAITMIWKGYPFVSIMTLAGLQS 228

Query: 184 IPEELYEAASIDGASRWQQFWSITLPLLTPALVVALIFRTLDALRVFDVVFVMSGVNP-- 241
           IPE+ Y AA +DGA+ +Q+FW IT+P+L P L V  +   L   R F ++ V++   P  
Sbjct: 229 IPEDFYNAAKVDGANAFQRFWYITIPVLMPVLGVTSVLVVLWVFRDFSIIKVLTDGGPLK 288

Query: 242 ATRTLAVYNRQTLVDFQDLGYGSAISVAILVIIFAFVLLYM 282
           AT+TL++        F ++GY SAI +  LV+     LL +
Sbjct: 289 ATQTLSIMTYDQAFGFFNMGYASAIGIVTLVLCVVASLLML 329


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: 266
Number of extensions: 10
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: 291
Length of database: 337
Length adjustment: 27
Effective length of query: 264
Effective length of database: 310
Effective search space:    81840
Effective search space used:    81840
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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