GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00900 in Halomonas xinjiangensis TRM 0175

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_043531487.1 JH15_RS14390 ABC transporter ATP-binding protein

Query= uniprot:A0A165KC78
         (242 letters)



>NCBI__GCF_000759345.1:WP_043531487.1
          Length = 234

 Score =  196 bits (497), Expect = 4e-55
 Identities = 100/233 (42%), Positives = 155/233 (66%), Gaps = 2/233 (0%)

Query: 9   LLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIEY 68
           LL+   +   YGG+  + GV+  +   ++  ++G NGAGK+T +KAI G L +N G I  
Sbjct: 3   LLEASDVHGGYGGMNILNGVNIAIEADQIGVIVGPNGAGKSTMLKAIFGLLEVNQGEIRL 62

Query: 69  LGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILADIEKMFTI 128
            G+ I       LV +G+  VP+ + +F  +++ ENL+MG YIR +    +  +E+++  
Sbjct: 63  RGEPITNLAPNKLVHKGMGFVPQEKNIFPSLSLQENLEMGTYIRPNNFRRM--LEQIYDF 120

Query: 129 FPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFEVVRDV 188
           FP L E++ Q AG +SGG++QM+AMGRALM++P VLLLDEP+ GLSP+ +++IFE V+ +
Sbjct: 121 FPPLVEKRHQPAGELSGGQRQMVAMGRALMAEPSVLLLDEPTAGLSPMYMNEIFERVKTI 180

Query: 189 YALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYLG 241
            A GV I++VEQ+A +ALAIA +G+V+ +G    T  G+ LLNDP V  ++LG
Sbjct: 181 NAAGVGILMVEQHAKQALAIAHKGFVLAAGQNRFTDTGEALLNDPDVAKSFLG 233


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: 156
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: 234
Length adjustment: 23
Effective length of query: 219
Effective length of database: 211
Effective search space:    46209
Effective search space used:    46209
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: 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