GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1693 in Desulfovibrio vulgaris Miyazaki F

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 8502040 DvMF_2753 ABC transporter related (RefSeq)

Query= uniprot:A0A165KC86
         (260 letters)



>FitnessBrowser__Miya:8502040
          Length = 255

 Score =  236 bits (601), Expect = 5e-67
 Identities = 122/248 (49%), Positives = 163/248 (65%)

Query: 9   VLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFEL 68
           +L +  ++K FGGL A+++V   +  G + GLIGPNGAGKTT FN+ITG Y PD+G    
Sbjct: 3   LLALRNLTKTFGGLVAVNNVTFDVAEGSIVGLIGPNGAGKTTVFNLITGNYKPDSGDIFF 62

Query: 69  AGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKGFK 128
            G+  +    H + + GIARTFQ IRLF  M+ +ENV+ G H R  SG+  A+ RT   +
Sbjct: 63  DGRTIKGLPTHRIVQQGIARTFQTIRLFQNMSVIENVLAGCHCRMQSGMLSAMLRTPAQR 122

Query: 129 AEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAGM 188
           AEE     RA   L++VG+       A+ LSYG+QR LEIARALATDP+ I LDEPA GM
Sbjct: 123 AEEQRALLRATRELEFVGLANEHANLAKNLSYGNQRLLEIARALATDPRFIILDEPAGGM 182

Query: 189 NATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQKNE 248
           N  E   L + I  IR+   T+LLIEHD+ LVM +C+++ VL+YG  +AEG PA ++ + 
Sbjct: 183 NDQETAALIDTIRAIRDRGITVLLIEHDMSLVMKVCEKLVVLEYGALLAEGVPAAIKDDP 242

Query: 249 KVIEAYLG 256
           +VIEAYLG
Sbjct: 243 RVIEAYLG 250


Lambda     K      H
   0.319    0.137    0.384 

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: 208
Number of extensions: 5
Number of successful extensions: 1
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: 260
Length of database: 255
Length adjustment: 24
Effective length of query: 236
Effective length of database: 231
Effective search space:    54516
Effective search space used:    54516
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 (21.7 bits)
S2: 47 (22.7 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