GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braC in Halomonas xinjiangensis TRM 0175

Align NatB, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate WP_043531481.1 JH15_RS14375 ABC transporter substrate-binding protein

Query= TCDB::Q8YVY4
         (441 letters)



>NCBI__GCF_000759345.1:WP_043531481.1
          Length = 399

 Score =  176 bits (446), Expect = 1e-48
 Identities = 133/398 (33%), Positives = 202/398 (50%), Gaps = 22/398 (5%)

Query: 44  ATDTTATSGGSGLKIGSLLPATGDLASIGQQMAAAVPLVVETVNACGGV-NGQPVSLVAV 102
           A  T A+   + +KIG L   TG + S+   + A   L V  +N  GG+ +G+ + +   
Sbjct: 11  AAATVASVAQADVKIGFLGGFTGPIESLTPPIYAGAQLAVSQINEQGGILDGETLVMPNA 70

Query: 103 DDQ-TDPKAGAAGMTKLATVDKVAGVVGSFASSVSTAAVSIAA-QNKVLLISPGSTSPVF 160
           D    D  A +    ++   +KV  +VG+  +  + AA + AA    V+++SP ST+P  
Sbjct: 71  DTTCADASAASNAADRMVNSEKVTAIVGALCTGATVAAANNAAIPGGVVMVSPASTAPAV 130

Query: 161 TEKAQKGDFNGFWARTVPPDSYQGPALAELANKKGFKRVSTIVINNDYGVGFEKAFVQAF 220
           TE     D N    RTVP D++QG  LA+L  +KG   V+   +NNDYG G   AF   F
Sbjct: 131 TEL----DDNDLVFRTVPSDAFQGEMLAKLLLEKGIDNVAVTYVNNDYGQGLADAFTTTF 186

Query: 221 EKLGGTVVNKNNPVRYDPKATTFETEAAAAFAGKPDAVLGVFYVET-GSLLLKSAYQQGV 279
           E  GGT+    N    D +A  + +E  +  +   + ++ + Y +T G  LL+ AY+ GV
Sbjct: 187 EDEGGTIA--ANQAHEDNRA-DYRSELGSLSSSGAETLVVLAYADTSGQTLLRQAYESGV 243

Query: 280 AQGVQIMLTDGMKSDEFPAQVGKTADGKFIASGIIGTVPGS-DGKGLEALTKLWQSKKGS 338
               Q +  DGM  +     VG  AD   +  G+I T PGS D  G E   ++  +    
Sbjct: 244 F--TQYVGADGMVGNSLVGAVG--AD---VLEGMIATRPGSPDLPGAEVFAEMANAADVD 296

Query: 339 APGEFAPQAWDATALLVLAAQAAKENTGVGIAGKIRDVSSAPGVEVT--DVCEGLKLLQE 396
               FA QA+DAT LL LA +    ++  G++  +RDV+ APG  +   +  +  +LL +
Sbjct: 297 PSAVFAAQAYDATFLLALAIEKNGSDSREGLSQALRDVAMAPGETILPGEWKKAKQLLAD 356

Query: 397 GKDINYQGASGNVDIDANGDVIGVYDVWTVGDDGKIKT 434
           G++INY+GASG  + D NGDV GV     V +DG   T
Sbjct: 357 GQEINYEGASGTHEFDDNGDVPGVVVEMAV-EDGSFVT 393


Lambda     K      H
   0.312    0.130    0.367 

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: 379
Number of extensions: 21
Number of successful extensions: 4
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: 441
Length of database: 399
Length adjustment: 32
Effective length of query: 409
Effective length of database: 367
Effective search space:   150103
Effective search space used:   150103
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 50 (23.9 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