GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08240 in Pseudomonas fluorescens FW300-N2E2

Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate Pf6N2E2_3578 Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)

Query= uniprot:G8ALI9
         (505 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3578
          Length = 426

 Score =  370 bits (949), Expect = e-107
 Identities = 180/319 (56%), Positives = 237/319 (74%), Gaps = 4/319 (1%)

Query: 149 RWLGPIAVVVALAFPFTPLADRQLLDIGILLLTYIMLGWGLNIVVGLAGLLDLGYVAFYA 208
           RW+ P  +V+A+ FPF   A++ +L + IL L Y++LG GLNIVVGLAGLLDLGYVAFYA
Sbjct: 97  RWIIPALIVIAIVFPF--FANKYVLTVVILGLIYVLLGLGLNIVVGLAGLLDLGYVAFYA 154

Query: 209 VGAYSYALLAHYFGFSFWVCLPLAGFLAAMSGVLLGFPVLRLRGDYFAIVTLGFGEIIRI 268
           +GAY  AL   Y G  FW  LPLA   AAM+G +LGFPVLR+ GDY AIVTLGFGEIIR+
Sbjct: 155 IGAYGLALGYQYLGLGFWTVLPLAAIAAAMAGCILGFPVLRMHGDYLAIVTLGFGEIIRL 214

Query: 269 ILINWYQFTGGPNGISGIPRPSFFGIADFTRTPAEGTAAFHEMFGLEFSPLHRIIFLYYL 328
           +L NW  FTGGPNG+  +P P+F G+ +F R   +G   FHE FG++++P  + +F+Y +
Sbjct: 215 VLNNWLSFTGGPNGMP-VPSPTFLGL-EFGRRAKDGGVPFHEFFGIDYNPNIKFLFIYIV 272

Query: 329 ILVLALVVNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMKLAAFAIAAMFGGFAG 388
           + +  L+V     R+ ++P+GRAWEALRED+IAC S+G+N   +KL+AF I A   G AG
Sbjct: 273 LFITVLLVLYVKHRLTRMPVGRAWEALREDEIACRSMGLNHVLVKLSAFTIGASTAGLAG 332

Query: 389 SFFATRQGFISPESFTFIESAIILAIVVLGGMGSQIGVVVAAFLVIGLPEAFRELADYRM 448
            FFA+ QGF++P SFTF ESA+ILAIVVLGGMGS +GVV+AAF++   PE  R  ++YR+
Sbjct: 333 VFFASYQGFVNPSSFTFFESALILAIVVLGGMGSTVGVVIAAFVLTVAPELLRSFSEYRV 392

Query: 449 LAFGMGMVLIMLWRPRGLL 467
           L FG+ MVL+M+WRPRGL+
Sbjct: 393 LLFGVLMVLMMIWRPRGLI 411


Lambda     K      H
   0.329    0.144    0.438 

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: 670
Number of extensions: 49
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 505
Length of database: 426
Length adjustment: 33
Effective length of query: 472
Effective length of database: 393
Effective search space:   185496
Effective search space used:   185496
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 (21.8 bits)
S2: 51 (24.3 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