GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS24015 in Rhodococcus qingshengii djl-6-2

Align ABC transporter related (characterized, see rationale)
to candidate WP_076948807.1 C1M55_RS07375 amino acid ABC transporter ATP-binding protein

Query= uniprot:B2TBJ9
         (263 letters)



>NCBI__GCF_002893965.1:WP_076948807.1
          Length = 261

 Score =  246 bits (627), Expect = 5e-70
 Identities = 129/248 (52%), Positives = 169/248 (68%), Gaps = 1/248 (0%)

Query: 8   ALSVKNIHKSFGDHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDDGSVSL 67
           A+  + IHKSFG   VL G+ L   +G+V  ILG SGSGKST LR LN LE  D G+V +
Sbjct: 12  AVEARGIHKSFGTLEVLAGVDLLVRKGEVTVILGPSGSGKSTLLRTLNHLEKVDRGTVRI 71

Query: 68  AGEELKMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPMRVQKRS 127
            GE +  +R+G+ +L     R++ + RS +G VFQNFNL+ H+T LEN++E P+  QKR 
Sbjct: 72  DGELIGYRRKGN-RLHELRDREILKQRSHIGFVFQNFNLFPHLTALENVVEAPLSAQKRD 130

Query: 128 RAESVEEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPTSALDP 187
           R E   EA ALL +VG+ EK   YP  LSGGQQQRVAIARALA+ P V+LFDEPTSALDP
Sbjct: 131 RDEVYREARALLERVGVGEKADEYPRQLSGGQQQRVAIARALALRPAVILFDEPTSALDP 190

Query: 188 ELVGEVLRVMRSLAEEGRTMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEVFVECKS 247
           ELVGEVL V+  LA +G T+++VTHE+GFAR V++  +F+  G +   G P +V      
Sbjct: 191 ELVGEVLEVLAQLARDGATLVIVTHEVGFAREVADTAVFMDGGVIVEQGPPSQVIDNPVH 250

Query: 248 DRFRQFVS 255
           +R + F+S
Sbjct: 251 ERTKAFLS 258


Lambda     K      H
   0.318    0.133    0.377 

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: 191
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: 263
Length of database: 261
Length adjustment: 25
Effective length of query: 238
Effective length of database: 236
Effective search space:    56168
Effective search space used:    56168
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 (21.7 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