GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03040 in Desulfovibrio vulgaris Miyazaki F

Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate 8500594 DvMF_1342 ABC transporter related (RefSeq)

Query= reanno::pseudo1_N1B4:Pf1N1B4_3435
         (254 letters)



>FitnessBrowser__Miya:8500594
          Length = 243

 Score =  226 bits (576), Expect = 3e-64
 Identities = 119/233 (51%), Positives = 159/233 (68%), Gaps = 13/233 (5%)

Query: 19  LKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLNNEELKLVANKDGALK 78
           L+GVSL  A G+V+ IIG SGSGKSTFLRC+N LE    G I +   ++           
Sbjct: 20  LRGVSLSVAPGEVVVIIGPSGSGKSTFLRCLNRLEYADEGAIRIEGRDI----------- 68

Query: 79  AADPK-QLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMSKTEAREKAEHYLNKV 137
             DP  ++  +R+ + MVFQ FNL+ H+T +EN+  A   V    K EA +K    L KV
Sbjct: 69  -LDPDCEINEVRAEVGMVFQSFNLFPHLTVLENLTLAQTTVRKRGKAEAEKKGMELLRKV 127

Query: 138 GVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPELVGDVLKVMQALAQ 197
           G+A + + YP  +SGG+QQRVAIARALAM+P+ MLFDEPTSALDPE+VG+VL VM+ LA+
Sbjct: 128 GIAEKHNVYPDQLSGGQQQRVAIARALAMDPKAMLFDEPTSALDPEMVGEVLDVMKNLAR 187

Query: 198 EGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQSERLQQFLS 250
           EG TMVVVTHEMGFAREV++++VF+ +G + E G+P +    P+ +R + FLS
Sbjct: 188 EGMTMVVVTHEMGFAREVADRVVFMDQGSILEVGSPDKFFTAPEHDRTKLFLS 240


Lambda     K      H
   0.317    0.131    0.366 

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: 184
Number of extensions: 7
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: 254
Length of database: 243
Length adjustment: 24
Effective length of query: 230
Effective length of database: 219
Effective search space:    50370
Effective search space used:    50370
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 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