GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_17600 in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align ABC transporter permease; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine ABC transporter permease HisM; SubName: Full=Histidine transport system permease protein; SubName: Full=Histidine/lysine/arginine/ornithine ABC transporter permease HisM (characterized, see rationale)
to candidate WP_068169957.1 HTA01S_RS09505 amino acid ABC transporter permease

Query= uniprot:A0A1N7U128
         (237 letters)



>NCBI__GCF_001592305.1:WP_068169957.1
          Length = 262

 Score =  102 bits (254), Expect = 7e-27
 Identities = 71/218 (32%), Positives = 106/218 (48%), Gaps = 13/218 (5%)

Query: 11  AYLFSDGAGLSGVAMTLWLFIISVVLGFFLSIPLALARVSEHVWLRWPVEVYTYLFRGTP 70
           A LF++G  L+ V +TL   +  +V+G    +  AL R S    +RW   +Y ++ RGTP
Sbjct: 51  AVLFAEGT-LATVQLTLTAGLAGIVIG----VLAALGRTSRIAPVRWFASLYVWVVRGTP 105

Query: 71  LYIQLLICYTGLYSLEIVQDNALLNQFFRNALNCTLLAFVLNTCAYTVEIFAGAIRNIPH 130
           L +Q+L  +  L +L       L  + F +A  C  LAF  N  AY  E     +  +P 
Sbjct: 106 LLVQILFVFLALPALV----PGLQLEDFASA--CVALAF--NVGAYNAEAIRSGLLAVPK 157

Query: 131 GEIEAARAYGLHGWRLNLFVVVPAALRRALPAYSNEMILMLHATSLAFTATVADILKVAR 190
           G+ EAAR+ GL  W   + V  P A + ALP   N  + +L  +SLA+   V ++  V  
Sbjct: 158 GQAEAARSLGLSSWHTFIDVSFPQAFKVALPPLVNNTVALLKDSSLAYAIGVVELTNVGN 217

Query: 191 DANAETFLTFQAFGIAALLYMLLSFALVGLFRLAERRW 228
              A TFL        AL+Y+ L+  L  +    ERR+
Sbjct: 218 RIQAATFLPLPTLATTALIYLTLTTVLTQISGAVERRY 255


Lambda     K      H
   0.332    0.143    0.443 

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: 151
Number of extensions: 8
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: 237
Length of database: 262
Length adjustment: 24
Effective length of query: 213
Effective length of database: 238
Effective search space:    50694
Effective search space used:    50694
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (22.0 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Apr 09 2024. 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