GapMind for catabolism of small carbon sources

 

Aligments for a candidate for cycA in Pseudomonas fluorescens FW300-N2E2

Align L-alanine and D-alanine permease (characterized)
to candidate Pf6N2E2_4959 S-methylmethionine permease

Query= reanno::pseudo5_N2C3_1:AO356_17670
         (473 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4959 S-methylmethionine
           permease
          Length = 476

 Score =  306 bits (783), Expect = 1e-87
 Identities = 163/441 (36%), Positives = 254/441 (57%), Gaps = 5/441 (1%)

Query: 19  KRELGERHIRLMALGACIGVGLFLGSAKAIEMAGP-AIMLSYIIGGLAILVIMRALGEMA 77
           K+E+  RHI ++ALG  IG GLFL S   +  AGP   +++YIIG L + ++M  LGE+A
Sbjct: 15  KQEMQTRHIVMLALGGVIGTGLFLTSGYTVNQAGPMGAVIAYIIGALMVYMVMMCLGELA 74

Query: 78  VHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWFPDVPRWIW 137
           V  P  GSFS YA  +LGP  G+   W YW  W V   +E TA  + M  WFPD P WIW
Sbjct: 75  VQMPETGSFSTYATRFLGPGTGYTVAWLYWLTWTVAIGSEFTAAGILMSRWFPDTPVWIW 134

Query: 138 ALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIA-MVIGGVGIIAFGFGNDGVALGIS 196
           +      +   N+I+V+ F E EFW +LIK++T++  ++IGG  I+     +   ++G+S
Sbjct: 135 SALFAGVVFLSNVISVRLFAETEFWLSLIKVLTVVVFLLIGGGAILGLLNIDQAHSIGLS 194

Query: 197 NLWAHGGFMPNGVSGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGSVFWRILL 256
           N    G F P G   + M+L  V FA+ G E+IG+ AGE K+PQ+ +P AI +   R+ +
Sbjct: 195 NFTREGLF-PTGFMPIAMTLLAVSFAFSGTELIGIAAGETKDPQRNVPRAIRTTVLRLAV 253

Query: 257 FYVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGGIFST 316
           F+VG +FV+ ++ P  + G   SPFV  F  +GI  +A I+NFV+I+A LS+ N G+++ 
Sbjct: 254 FFVGTIFVLATLLPREQAGLVESPFVTVFTYIGIPYSADIMNFVIISALLSAANSGLYAA 313

Query: 317 GRMLYSLAQNGQAPAGFAKTSTNGVPRRALLLSIAALLLGVLLNYLVPEKVFVWVTSIAT 376
            RML++L+  G  P  F+  +  G P  A+++S+A     +L +    + +++ + SI+ 
Sbjct: 314 SRMLWTLSDQGHLPKQFSALTRMGTPLNAIIVSMAGGAASLLSSVFAADTIYLALVSISG 373

Query: 377 FGAIWTWVMILLAQLKFRKSLSAS--ERAALKYRMWLYPVSSYLALAFLVLVVGLMAYFP 434
              +  W+ I  +Q+ FR+   A+  +   LK+R+  YP     AL    L    +A+ P
Sbjct: 374 LAVVVVWMSIAASQIAFRRHYVANGGDIRKLKFRVRGYPWVPLGALVCCSLACIGIAFDP 433

Query: 435 DTRVALYVGPAFLVLLTVLFY 455
           + RVALY G  F+     ++Y
Sbjct: 434 EQRVALYFGLPFIAWCYFVYY 454


Lambda     K      H
   0.328    0.142    0.444 

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: 606
Number of extensions: 25
Number of successful extensions: 5
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: 473
Length of database: 476
Length adjustment: 33
Effective length of query: 440
Effective length of database: 443
Effective search space:   194920
Effective search space used:   194920
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: 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 paper from 2022 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