GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4959
          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:

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