GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00900 in Shewanella halifaxensis HAW-EB4

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_012275875.1 SHAL_RS03825 ABC transporter ATP-binding protein

Query= uniprot:D8IUY7
         (241 letters)



>NCBI__GCF_000019185.1:WP_012275875.1
          Length = 314

 Score = 91.7 bits (226), Expect = 2e-23
 Identities = 65/192 (33%), Positives = 104/192 (54%), Gaps = 7/192 (3%)

Query: 6   LKVQQLSVAY-GGIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRVEGHI 64
           L +  L   Y GG++AVKGI L VN+G+   L+G NGAGK+TT+  I+  +  S   G +
Sbjct: 8   LVIDSLKKTYKGGVEAVKGISLTVNKGDFFALLGPNGAGKSTTIGVISSLVQKSA--GKV 65

Query: 65  EYLGQPLKGKKSFELVKDKLAMVPEGRGVFTRMSIQENLLMGAYTSDDKGQIA-ADIDKW 123
                 +   K  EL K  + +VP+        ++ + ++  A     K  +A A  +K+
Sbjct: 66  SVFEHDID--KELELAKLCIGLVPQEFNFNQFETVLQIVVNQAGYYGVKRDVALARAEKY 123

Query: 124 FAVFPRLKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVEKIFEVI 183
            +    L E+    A  LSGG ++ L +ARALM  PKLL+LDEP+ G+   +   ++  +
Sbjct: 124 LSQLD-LWEKRNSAARELSGGMKRRLMIARALMHEPKLLILDEPTAGVDIELRRSMWTFL 182

Query: 184 RNVSAQGITILL 195
             ++AQG+TI+L
Sbjct: 183 TELNAQGVTIIL 194


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: 166
Number of extensions: 6
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 241
Length of database: 314
Length adjustment: 25
Effective length of query: 216
Effective length of database: 289
Effective search space:    62424
Effective search space used:    62424
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: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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