GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuF in Sinorhizobium fredii NGR234

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 WP_015888140.1 NGR_RS09950 sugar ABC transporter permease

Query= TCDB::Q72H67
         (291 letters)



>NCBI__GCF_000018545.1:WP_015888140.1
          Length = 307

 Score =  209 bits (531), Expect = 8e-59
 Identities = 111/277 (40%), Positives = 172/277 (62%), Gaps = 4/277 (1%)

Query: 9   LAWILVLPTLLVVVLVAGYPLAQVFYWSFFKADIAFVEPPEFVGLENYAYLFQDPDFRQA 68
           L ++++ PT+L+++ +  +P   +FY +  +       P EFVG+ N+A L  DP F  A
Sbjct: 27  LRYLMLAPTVLILLALTIFPSIYMFYAAVHRISPNPDLPWEFVGVGNFARLLSDPQFHVA 86

Query: 69  LWNTLKFTVVSVSLETVLGLAIALIIHSNFRGRGLVRTAILIPWAIPTVVSAKMWQWMLN 128
           L NT+ FT+V+V+LE +LGL +AL++    R    ++T ++IP  +P +  A  W+ +  
Sbjct: 87  LRNTVVFTLVAVALEFLLGLGLALLLDRFIRRLSFLKTVLMIPMMLPPIAVAITWKLIYE 146

Query: 129 DVYGVINVLGVKLGLLSQKVAFLARPELLLPSIIAVDVWKTTPFMALLLLAGLQMIPEEL 188
             +GV+N +   LGL  Q  A+     L + SII  DVW+ TPF+ LL+LAGL  +P E 
Sbjct: 147 PQFGVLNEIMFLLGLPVQ--AWAGDVNLAMFSIIVADVWQWTPFVFLLMLAGLASLPVEP 204

Query: 189 YEAASIDGASRWQQFWSITLPLLTPALVVALIFRTLDALRVFDVVFVMSGVNPATRT--L 246
           YEAA++DGAS W+QFW +TLP L P + +AL+ R +DALR+FD+VF+++G  PA RT  L
Sbjct: 205 YEAAALDGASSWRQFWDLTLPFLKPVIAIALLLRVMDALRLFDLVFILTGGGPADRTKVL 264

Query: 247 AVYNRQTLVDFQDLGYGSAISVAILVIIFAFVLLYMR 283
           ++Y  Q    F D GY +AIS+ +L +       +M+
Sbjct: 265 SLYIYQVAYRFADPGYAAAISLFVLFVTIVLSTWFMK 301


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: 257
Number of extensions: 14
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: 307
Length adjustment: 27
Effective length of query: 264
Effective length of database: 280
Effective search space:    73920
Effective search space used:    73920
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 Apr 09 2024. 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