GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltL in Rhodococcus qingshengii djl-6-2

Align GluA aka CGL1950, component of Glutamate porter (characterized)
to candidate WP_076948807.1 C1M55_RS07375 amino acid ABC transporter ATP-binding protein

Query= TCDB::P48243
         (242 letters)



>NCBI__GCF_002893965.1:WP_076948807.1
          Length = 261

 Score =  258 bits (660), Expect = 6e-74
 Identities = 128/249 (51%), Positives = 172/249 (69%), Gaps = 10/249 (4%)

Query: 2   IKMTGVQKYFGDFHALTDIDLEIPRGQVVVVLGPSGSGKSTLCRTINRLETIEEGTIEID 61
           ++  G+ K FG    L  +DL + +G+V V+LGPSGSGKSTL RT+N LE ++ GT+ ID
Sbjct: 13  VEARGIHKSFGTLEVLAGVDLLVRKGEVTVILGPSGSGKSTLLRTLNHLEKVDRGTVRID 72

Query: 62  GKVLPEEGKG----------LANLRADVGMVFQSFNLFPHLTIKDNVTLAPIKVRKMKKS 111
           G+++    KG          +   R+ +G VFQ+FNLFPHLT  +NV  AP+  +K  + 
Sbjct: 73  GELIGYRRKGNRLHELRDREILKQRSHIGFVFQNFNLFPHLTALENVVEAPLSAQKRDRD 132

Query: 112 EAEKLAMSLLERVGIANQADKYPAQLSGGQQQRVAIARALAMNPKIMLFDEPTSALDPEM 171
           E  + A +LLERVG+  +AD+YP QLSGGQQQRVAIARALA+ P ++LFDEPTSALDPE+
Sbjct: 133 EVYREARALLERVGVGEKADEYPRQLSGGQQQRVAIARALALRPAVILFDEPTSALDPEL 192

Query: 172 VNEVLDVMASLAKEGMTMVCVTHEMGFARKAADRVLFMADGLIVEDTEPDSFFTNPKSDR 231
           V EVL+V+A LA++G T+V VTHE+GFAR+ AD  +FM  G+IVE   P     NP  +R
Sbjct: 193 VGEVLEVLAQLARDGATLVIVTHEVGFAREVADTAVFMDGGVIVEQGPPSQVIDNPVHER 252

Query: 232 AKDFLGKIL 240
            K FL ++L
Sbjct: 253 TKAFLSRVL 261


Lambda     K      H
   0.319    0.135    0.379 

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: 167
Number of extensions: 5
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: 261
Length adjustment: 24
Effective length of query: 218
Effective length of database: 237
Effective search space:    51666
Effective search space used:    51666
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 46 (22.3 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