GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Kocuria flava HO-9041

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_083529437.1 AS188_RS12245 ATP-binding cassette domain-containing protein

Query= uniprot:A0A165KC78
         (242 letters)



>NCBI__GCF_001482365.1:WP_083529437.1
          Length = 313

 Score =  110 bits (274), Expect = 4e-29
 Identities = 66/222 (29%), Positives = 109/222 (49%), Gaps = 7/222 (3%)

Query: 9   LLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIEY 68
           +L+ +GL  A+GG   V+ V F V  G +   +G+NGAGKTTTM+ +TG L    G + +
Sbjct: 22  VLEARGLSRAFGGRTVVEDVSFRVEPGRMTGFVGANGAGKTTTMRMLTGVLRTTAGEVLW 81

Query: 69  LGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENL-QMGAYIRKDKAGILADIEKMFT 127
            G+ +         + G   +PE RG++ R  + + L  +G     D+   LA+  ++  
Sbjct: 82  DGRPVTAAD-----RAGFGYMPEERGLYPRQPVLDQLCYLGRLHGMDRRAALAEARRLLE 136

Query: 128 IFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFEVVRD 187
                   +D L GT+S G QQ + +  AL+  P  L+LDEP  GL P+ VD +  ++R+
Sbjct: 137 RLDLAGRERDPL-GTLSLGNQQRVQIAAALLHGPTALVLDEPFSGLDPVAVDAMTGLLRE 195

Query: 188 VYALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQL 229
               GV ++           + D   V+ +G +   G  + L
Sbjct: 196 RLEQGVPVLFSSHQLDLVDRLCDSLVVLSAGRVLAAGAVEDL 237


Lambda     K      H
   0.317    0.136    0.373 

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: 170
Number of extensions: 6
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: 242
Length of database: 313
Length adjustment: 25
Effective length of query: 217
Effective length of database: 288
Effective search space:    62496
Effective search space used:    62496
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: 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