GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS24015 in Halomonas xinjiangensis TRM 0175

Align ABC transporter related (characterized, see rationale)
to candidate WP_043532174.1 JH15_RS16045 ATP-binding cassette domain-containing protein

Query= uniprot:B2TBJ9
         (263 letters)



>NCBI__GCF_000759345.1:WP_043532174.1
          Length = 262

 Score =  293 bits (750), Expect = 2e-84
 Identities = 147/250 (58%), Positives = 188/250 (75%)

Query: 7   VALSVKNIHKSFGDHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDDGSVS 66
           +A+  +++ K +G+  VL  +SL      V+SI+G+SGSGKST LRC+NLLE PD G ++
Sbjct: 11  LAVDARHLQKHYGEVPVLHDVSLSVTDRHVVSIIGSSGSGKSTLLRCMNLLEIPDRGELT 70

Query: 67  LAGEELKMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPMRVQKR 126
           +A E ++ +R   G     DRRQV ++RSQ+ MVFQ FNLW H++VL N+IE P+RV   
Sbjct: 71  IANEAIRFQRNAQGDNVGIDRRQVHKLRSQVSMVFQQFNLWPHLSVLGNVIEAPLRVHGL 130

Query: 127 SRAESVEEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPTSALD 186
           SR E++E  E  LAKVGLA+KR  +P+ LSGGQQQRVAIARALAM P+V+LFDEPTSALD
Sbjct: 131 SRREAIERGEHYLAKVGLADKRNAFPSFLSGGQQQRVAIARALAMEPRVLLFDEPTSALD 190

Query: 187 PELVGEVLRVMRSLAEEGRTMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEVFVECK 246
           PELV EVL V+  LA EGRTML+VTHEM FAR VSN ++FLHQG VE  G+P +VF + +
Sbjct: 191 PELVNEVLGVIGGLAGEGRTMLLVTHEMSFAREVSNEIVFLHQGHVEEAGSPQQVFEQAR 250

Query: 247 SDRFRQFVSS 256
           SDR RQF+SS
Sbjct: 251 SDRCRQFLSS 260


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: 227
Number of extensions: 4
Number of successful extensions: 1
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: 262
Length adjustment: 25
Effective length of query: 238
Effective length of database: 237
Effective search space:    56406
Effective search space used:    56406
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