GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_17600 in Pseudomonas stutzeri RCH2

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 GFF136 Psest_0136 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family

Query= uniprot:A0A1N7U128
         (237 letters)



>FitnessBrowser__psRCH2:GFF136
          Length = 229

 Score =  166 bits (420), Expect = 4e-46
 Identities = 89/211 (42%), Positives = 135/211 (63%), Gaps = 2/211 (0%)

Query: 20  LSGVAMTLWLFIISVVLGFFLSIPLALARVSEHVWLRWPVEVYTYLFRGTPLYIQLLICY 79
           + G  +TL L  +SV+ G  +++PL +AR S H+ +R     Y + FRGTPL +QL + Y
Sbjct: 14  IDGAWLTLQLVGVSVIAGLIVAVPLGIARSSRHLAVRALPYGYIFFFRGTPLLVQLFLVY 73

Query: 80  TGLYSLEIVQDNALLNQFFRNALNCTLLAFVLNTCAYTVEIFAGAIRNIPHGEIEAARAY 139
            G+   ++V+ +AL   + R+   C ++   L+T AY  EI  GAI+N+PHGEIEAARA 
Sbjct: 74  YGMAQFDVVRQSALW-PYLRDPYWCAIITMTLHTAAYIAEIIRGAIQNVPHGEIEAARAL 132

Query: 140 GLHGWRLNLFVVVPAALRRALPAYSNEMILMLHATSLAFTATVADILKVARDANAETFLT 199
           G+   +  L +++P A R  LPAYSNE+ILML A++LA T T+ ++  +AR   A T+L 
Sbjct: 133 GMSRSQALLHIILPRATRIGLPAYSNEVILMLKASALASTITLLELTGMARKIAARTYLH 192

Query: 200 FQAFGIAALLYMLLSFALVGLFRLAERRWMR 230
            + F  A L+Y+L++F L+  F+L E RW+R
Sbjct: 193 EEMFLTAGLIYLLIAFILMQGFKLLE-RWLR 222


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: 193
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: 229
Length adjustment: 23
Effective length of query: 214
Effective length of database: 206
Effective search space:    44084
Effective search space used:    44084
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 Sep 17 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