GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuF in Desulfovibrio vulgaris Miyazaki F

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 8499892 DvMF_0657 binding-protein-dependent transport systems inner membrane component (RefSeq)

Query= TCDB::Q72H67
         (291 letters)



>FitnessBrowser__Miya:8499892
          Length = 297

 Score =  162 bits (409), Expect = 1e-44
 Identities = 93/271 (34%), Positives = 145/271 (53%), Gaps = 6/271 (2%)

Query: 3   TLRQVRLAWILVLPTLLVVVLVAGYPLAQVFYWSFFKADIAFVEPPEFVGLENYAYLFQD 62
           T+R +  AW+L+LP L  +     YP    F  SFF  D     P +FVGLE+Y YL +D
Sbjct: 10  TMRTIH-AWLLLLPALAFIAAFTHYPAVNTFIHSFF-LDGRGGAPAQFVGLEHYQYLLED 67

Query: 63  PDFRQALWNTLKFTVVSVSLETVLGLAIALIIHSNFRGRGLVRTAILIPWAIPTVVSAKM 122
             FR+AL N L F   ++ L   L + +A ++++   G+ ++R    +P  +P +  A +
Sbjct: 68  EVFRKALVNNLLFASGTIPLSIGLAMTMAFLVNAGLAGQSVLRLCYFVPTVLPMIAVANI 127

Query: 123 WQWMLNDVYGVINVLGVKLGLLSQKVAFLARPELLLPSIIAVDVWKTTPFMALLLLAGLQ 182
           W +     YG++  +   LGL    V +L      LP +IAV VWK   F  +  LA LQ
Sbjct: 128 WLFFYTPEYGLLEQIRGALGLAG--VNWLGSESTALPCVIAVAVWKDAGFFMIFYLAALQ 185

Query: 183 MIPEELYEAASIDGASRWQQFWSITLPLLTPALVVALIFRTLDALRVFDVVFVMS--GVN 240
            IP  L EAA ++GASR   +  + +PLL P  +  L+  T++A R+ D +FV++  G N
Sbjct: 186 QIPPSLGEAAMLEGASRLYYYRRVVIPLLMPTTLFVLVNATINAFRMVDHLFVLTQGGPN 245

Query: 241 PATRTLAVYNRQTLVDFQDLGYGSAISVAIL 271
            A+  L  Y  +    + D GYG+A+++ +L
Sbjct: 246 NASSLLLYYIYEVSFKYWDTGYGAALTMVLL 276


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: 225
Number of extensions: 14
Number of successful extensions: 4
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: 297
Length adjustment: 26
Effective length of query: 265
Effective length of database: 271
Effective search space:    71815
Effective search space used:    71815
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