GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00900 in Rhizorhabdus wittichii RW1

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_041378948.1 SWIT_RS04010 ABC transporter ATP-binding protein

Query= uniprot:D8IUY7
         (241 letters)



>NCBI__GCF_000016765.1:WP_041378948.1
          Length = 252

 Score = 90.9 bits (224), Expect = 2e-23
 Identities = 71/230 (30%), Positives = 112/230 (48%), Gaps = 16/230 (6%)

Query: 15  YGGIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRVEGHIEYLGQPLKGK 74
           Y G   +  + L +  G  V L+GA+GAGKTT LKAI   +      G I   G+ +  +
Sbjct: 11  YAGRHVLDDVSLTIERGSFVALVGASGAGKTTLLKAINRLVEID--TGTIAIEGRDVAAQ 68

Query: 75  KSFELVKDKLAMVPEGRGVFTRMSIQENL-----LMGAYTSDDKGQIAADIDKWFAVFPR 129
              EL + ++  V +G G+F  MS+ EN+     L G    +   ++A  +D        
Sbjct: 69  PVAEL-RRRIGYVFQGIGLFPHMSVAENVALVPRLQGVPREERAARVAELLDLVALPADF 127

Query: 130 LKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVEKIFEVIRNV-SA 188
            + R AQ    LSGG+ Q +  ARAL + P ++L+DEP   L P+  +++    R +  A
Sbjct: 128 AERRPAQ----LSGGQAQRVGFARALAARPAIMLMDEPFGALDPVTRDELGAAYRALHEA 183

Query: 189 QGITILLVEQNAKLALEAAHRGYVMESGLITMQGQAQQML---DDPRVKA 235
            G+T L+V  +   AL  A R  V+  G I      + ++    DPR++A
Sbjct: 184 MGLTSLIVTHDMAEALLLADRVIVIGEGRILADQPPRALIHGAGDPRIEA 233


Lambda     K      H
   0.317    0.134    0.365 

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: 155
Number of extensions: 8
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: 241
Length of database: 252
Length adjustment: 24
Effective length of query: 217
Effective length of database: 228
Effective search space:    49476
Effective search space used:    49476
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 (21.6 bits)
S2: 46 (22.3 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