GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Streptococcus massiliensis 4401825

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_018371968.1 BN415_RS05940 ABC transporter ATP-binding protein

Query= uniprot:A0A165KC78
         (242 letters)



>NCBI__GCF_000341525.1:WP_018371968.1
          Length = 296

 Score = 96.7 bits (239), Expect = 5e-25
 Identities = 67/221 (30%), Positives = 118/221 (53%), Gaps = 15/221 (6%)

Query: 9   LLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIEY 68
           L+ VK L  +  G + +K + F++ +G+ V+LIG NGAGKTT M  + G   +  G +  
Sbjct: 3   LITVKNLAKSIRGKEILKKISFDIEDGDCVALIGPNGAGKTTLMDCLLGDKFVTSGEV-- 60

Query: 69  LGKSIKG-KGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILAD--IEKM 125
              +IKG +   D +K  + ++P+   V A++ + E ++   + ++     L+D  ++K+
Sbjct: 61  ---AIKGLQPTDDKLKVSVAVLPQENAVPAKLKVKELIR---FFQEVYPNSLSDQEVDKL 114

Query: 126 FTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFEVV 185
                +   +KDQLA  +SGG++++L+    L+ +PK+L LDEP+  +      + +E+V
Sbjct: 115 LRFSDK---QKDQLAEKLSGGQKRLLSFVLTLIGRPKILFLDEPTASMDTSTRQRFWEIV 171

Query: 186 RDVYALGVTIVLVEQNASRALAIADRGYVMESG-LITMTGP 225
            ++ A  VTIV            ADR  V+  G LI  T P
Sbjct: 172 AELKAQDVTIVYSSHYIEEVEHTADRILVLHKGELIRDTTP 212


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: 153
Number of extensions: 10
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: 296
Length adjustment: 25
Effective length of query: 217
Effective length of database: 271
Effective search space:    58807
Effective search space used:    58807
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