GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_17115 AO353_17115
           leucine/isoleucine/valine transporter permease subunit
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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