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_2924 Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)

Query= uniprot:G8ALI9
         (505 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2924
          Length = 418

 Score =  414 bits (1063), Expect = e-120
 Identities = 207/324 (63%), Positives = 252/324 (77%), Gaps = 3/324 (0%)

Query: 149 RWLGPIAVVVALAFPFTPLADRQLLDIGILLLTYIMLGWGLNIVVGLAGLLDLGYVAFYA 208
           RW+    +V AL +PF     R  +DI  L+L Y+MLG GLNIVVGLAGLLDLGYV FYA
Sbjct: 92  RWIVLALIVGALVWPF--FGSRGAVDIATLILIYVMLGLGLNIVVGLAGLLDLGYVGFYA 149

Query: 209 VGAYSYALLAHYFGFSFWVCLPLAGFLAAMSGVLLGFPVLRLRGDYFAIVTLGFGEIIRI 268
           VGAYSYALL+HYFG SFW+CLP+AG +AA  G LLGFPVLRLRGDY AIVTLGFGEIIR+
Sbjct: 150 VGAYSYALLSHYFGLSFWICLPIAGMMAATFGFLLGFPVLRLRGDYLAIVTLGFGEIIRL 209

Query: 269 ILINWYQFTGGPNGISGIPRPSFFGIADFTRTPAEGTAAFHEMFGLEFSPLHRIIFLYYL 328
            L N    TGGPNGIS I +P+FFG+  F R  AEG   FHE FGLE++ ++++IFLY +
Sbjct: 210 FLRNLTDITGGPNGISNIEKPTFFGLT-FERKAAEGLQTFHEYFGLEYNSINKVIFLYLV 268

Query: 329 ILVLALVVNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMKLAAFAIAAMFGGFAG 388
            L+LAL       R+ ++P+GRAWEALRED+IAC +LG+N T +KL+AF + A F GFAG
Sbjct: 269 ALLLALAALFVINRLLRMPIGRAWEALREDEIACRALGLNPTVIKLSAFTLGAAFAGFAG 328

Query: 389 SFFATRQGFISPESFTFIESAIILAIVVLGGMGSQIGVVVAAFLVIGLPEAFRELADYRM 448
           SFFA RQG ++PESFTFIESAIILAIVVLGGMGSQ+GV++AA ++I LPE  RE ++YRM
Sbjct: 329 SFFAARQGLVTPESFTFIESAIILAIVVLGGMGSQLGVILAAIVMILLPEMMREFSEYRM 388

Query: 449 LAFGMGMVLIMLWRPRGLLAHRDP 472
           L FG  MVL+M+WRP+GLL  + P
Sbjct: 389 LMFGALMVLMMIWRPQGLLPMQRP 412


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: 623
Number of extensions: 35
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: 505
Length of database: 418
Length adjustment: 33
Effective length of query: 472
Effective length of database: 385
Effective search space:   181720
Effective search space used:   181720
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