GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08240 in Pseudomonas fluorescens FW300-N2E3

Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate AO353_17115 AO353_17115 leucine/isoleucine/valine transporter permease subunit

Query= uniprot:G8ALI9
         (505 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_17115
          Length = 418

 Score =  415 bits (1066), Expect = e-120
 Identities = 220/399 (55%), Positives = 280/399 (70%), Gaps = 7/399 (1%)

Query: 78  AVTVLVLAAAATAAGFFIAMPTEALRVILI-AGGAVIAIRAVLAIRTGRSKLSQAERDKR 136
           AV   VL    + AG  + +       +LI A  +V+    VL  R   + +    + K 
Sbjct: 17  AVAYPVLGLKLSIAGINLEVQGATTSTLLIIAACSVLMFLRVLFDREYTAAMRSVPKGKL 76

Query: 137 MDHIAAQ---VQHASRWLGPIAVVVALAFPFTPLADRQLLDIGILLLTYIMLGWGLNIVV 193
           +   A+    +    RW+    +V+AL +PF     R  +DI  L+L Y++LG GLNIVV
Sbjct: 77  IPASASNFLTLPSTQRWVIMGLIVIALVWPF--FGSRGAVDIATLILIYVLLGLGLNIVV 134

Query: 194 GLAGLLDLGYVAFYAVGAYSYALLAHYFGFSFWVCLPLAGFLAAMSGVLLGFPVLRLRGD 253
           GLAGLLDLGYV FYAVGAYSYALL+HY+G SFW+CLP+AG +AA  G LLGFPVLRLRGD
Sbjct: 135 GLAGLLDLGYVGFYAVGAYSYALLSHYYGLSFWICLPIAGLMAATFGFLLGFPVLRLRGD 194

Query: 254 YFAIVTLGFGEIIRIILINWYQFTGGPNGISGIPRPSFFGIADFTRTPAEGTAAFHEMFG 313
           Y AIVTLGFGEIIR+ L N    TGGPNGIS IP+PS FG++ F RT AEG   FHE FG
Sbjct: 195 YLAIVTLGFGEIIRLFLRNLTGLTGGPNGISNIPKPSLFGLS-FERTAAEGMQTFHEFFG 253

Query: 314 LEFSPLHRIIFLYYLILVLALVVNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMK 373
           L ++P+ +++FLY + L+LAL       R+ ++P+GRAWEALRED+IAC +LG+N T +K
Sbjct: 254 LTYNPVSKVVFLYLVALLLALFALFVINRLLRMPIGRAWEALREDEIACRALGLNPTVIK 313

Query: 374 LAAFAIAAMFGGFAGSFFATRQGFISPESFTFIESAIILAIVVLGGMGSQIGVVVAAFLV 433
           L+AF + A F GFAGSFFA RQG ++PESFTFIESA ILAIVVLGGMGSQ+GVV+AA ++
Sbjct: 314 LSAFTLGACFAGFAGSFFAARQGLVTPESFTFIESATILAIVVLGGMGSQLGVVLAAVVM 373

Query: 434 IGLPEAFRELADYRMLAFGMGMVLIMLWRPRGLLAHRDP 472
           I LPE  R+ ++YRML FG  MVL+M+WRP+GLL  + P
Sbjct: 374 ILLPELMRDFSEYRMLMFGALMVLMMIWRPQGLLPMQRP 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: 608
Number of extensions: 34
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