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_068169050.1 HTA01S_RS08125 ABC transporter permease subunit

Query= uniprot:A0A1N7U128
         (237 letters)



>NCBI__GCF_001592305.1:WP_068169050.1
          Length = 238

 Score =  183 bits (464), Expect = 3e-51
 Identities = 98/218 (44%), Positives = 140/218 (64%), Gaps = 4/218 (1%)

Query: 21  SGVAMTLWLFIISVVLGFFLSIPLALARVSEHVWLRWPVEVYTYLFRGTPLYIQLLICYT 80
           +G+  T+ L  +S++ G  L++PL L RVS + W+  P+ ++TY+ RGTPL IQ+   Y 
Sbjct: 18  TGLIATMELLGVSLIAGALLTLPLTLMRVSRNRWVSSPIWLFTYVVRGTPLLIQVYFIYY 77

Query: 81  GLYSLEIVQ---DNALLNQFFRNALNCTLLAFVLNTCAYTVEIFAGAIRNIPHGEIEAAR 137
           G+  LE VQ   D      +F++   C +LAF LNTCAYTVE+ AGAI+  P GEIEAA+
Sbjct: 78  GIAQLEWVQGLWDTHWPFTWFKDPFFCAVLAFTLNTCAYTVEMLAGAIKETPAGEIEAAQ 137

Query: 138 AYGLHGWRLNLFVVVPAALRRALPAYSNEMILMLHATSLA-FTATVADILKVARDANAET 196
           A G   W +   +++P+A+RR LP YSNE+++MLHATSLA     + D+   A       
Sbjct: 138 AAGFGKWNMMFRLILPSAMRRTLPGYSNEVVMMLHATSLASVVPALYDLTNAAYAIYKTY 197

Query: 197 FLTFQAFGIAALLYMLLSFALVGLFRLAERRWMRFLVP 234
           +L FQ F   A+LY +L+FALV +FRL ERR++ +L P
Sbjct: 198 YLAFQPFIFVAVLYFMLTFALVYVFRLLERRFLAYLRP 235


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: 195
Number of extensions: 10
Number of successful extensions: 3
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: 238
Length adjustment: 23
Effective length of query: 214
Effective length of database: 215
Effective search space:    46010
Effective search space used:    46010
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