GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araH in Pseudomonas simiae WCS417

Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate GFF2163 PS417_11035 arabinose ABC transporter permease

Query= CharProtDB::CH_014278
         (328 letters)



>FitnessBrowser__WCS417:GFF2163
          Length = 322

 Score =  377 bits (967), Expect = e-109
 Identities = 186/301 (61%), Positives = 233/301 (77%)

Query: 23  DQYGMLVVFAVLFIACAIFVPNFATFINMKGLGLAISMSGMVACGMLFCLASGDFDLSVA 82
           D + ML+    +F+ CA+ + NF + +NM+GLGLAIS  G+ AC MLFCLASG FDLSV 
Sbjct: 22  DNWAMLLAAVSIFLLCALLIDNFLSPLNMRGLGLAISTVGIAACTMLFCLASGHFDLSVG 81

Query: 83  SVIACAGVTTAVVINLTESLWIGVAAGLLLGVLCGLVNGFVIAKLKINALITTLATMQIV 142
           SVIACAGV  A+V+  T+S+ +G+ A LL+G++ GL+NG VIAKL++NALITTLATMQIV
Sbjct: 82  SVIACAGVVAAIVMRDTDSVMLGIGAALLMGLMVGLINGIVIAKLRVNALITTLATMQIV 141

Query: 143 RGLAYIISDGKAVGIEDESFFALGYANWFGLPAPIWLTVACLIIFGLLLNKTTFGRNTLA 202
           RGLAYI ++GKAVG+  + FF  G     G+P PI +T+ C + FG LLN TT+GRNT+A
Sbjct: 142 RGLAYIFANGKAVGVSQDQFFVFGNGQLMGVPVPILITILCFLFFGWLLNYTTYGRNTMA 201

Query: 203 IGGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILASRMTSGQPMTSIGYELIVISAC 262
           IGGN EAA LAGV V RTKI+IF + G++ A+AG+ILASRMTSGQPM   G+EL VISAC
Sbjct: 202 IGGNPEAALLAGVNVDRTKILIFAVHGVIGALAGVILASRMTSGQPMIGQGFELTVISAC 261

Query: 263 VLGGVSLKGGIGKISYVVAGILILGTVENAMNLLNISPFAQYVVRGLILLAAVIFDRYKQ 322
           VLGGVSL GG+G I +V+AG+LIL  +ENAMNL NI  F QYV+RG ILL AV+ DR KQ
Sbjct: 262 VLGGVSLSGGVGMIRHVIAGVLILAIIENAMNLKNIDTFYQYVIRGSILLLAVVIDRMKQ 321

Query: 323 K 323
           +
Sbjct: 322 R 322


Lambda     K      H
   0.327    0.141    0.414 

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: 394
Number of extensions: 11
Number of successful extensions: 1
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: 328
Length of database: 322
Length adjustment: 28
Effective length of query: 300
Effective length of database: 294
Effective search space:    88200
Effective search space used:    88200
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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