GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysP in Pseudomonas fluorescens FW300-N2E2

Align lysine-specific permease (characterized)
to candidate Pf6N2E2_4959 S-methylmethionine permease

Query= CharProtDB::CH_003129
         (489 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4959
          Length = 476

 Score =  379 bits (974), Expect = e-110
 Identities = 198/480 (41%), Positives = 290/480 (60%), Gaps = 19/480 (3%)

Query: 2   VSETKTTEAPGLRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYMLIGLM 61
           + E +     G ++E++ RH+ M+A+GG IGTGLF+ SG T++QAGP GA+++Y++  LM
Sbjct: 3   IKEQQLNTRAGFKQEMQTRHIVMLALGGVIGTGLFLTSGYTVNQAGPMGAVIAYIIGALM 62

Query: 62  VYFLMTSLGELAAYMPVSGSFATYGQNYVEEGFGFALGWNYWYNWAVTIAVDLVAAQLVM 121
           VY +M  LGELA  MP +GSF+TY   ++  G G+ + W YW  W V I  +  AA ++M
Sbjct: 63  VYMVMMCLGELAVQMPETGSFSTYATRFLGPGTGYTVAWLYWLTWTVAIGSEFTAAGILM 122

Query: 122 SWWFPDTPGWIWSALFLGVIFLLNYISVRGFGEAEYWFSLIKVTTVIVFIIVGVLMIIGI 181
           S WFPDTP WIWSALF GV+FL N ISVR F E E+W SLIKV TV+VF+++G   I+G+
Sbjct: 123 SRWFPDTPVWIWSALFAGVVFLSNVISVRLFAETEFWLSLIKVLTVVVFLLIGGGAILGL 182

Query: 182 FK--GAQPAGWSNWTIGEAPFAGGFAAMIGVAMIVGFSFQGTELIGIAAGESEDPAKNIP 239
                A   G SN+T  E  F  GF  +    + V F+F GTELIGIAAGE++DP +N+P
Sbjct: 183 LNIDQAHSIGLSNFT-REGLFPTGFMPIAMTLLAVSFAFSGTELIGIAAGETKDPQRNVP 241

Query: 240 RAVRQVFWRILLFYVFAILIISLIIPYTDPSLLRNDVKDISVSPFTLVFQHAGLLSAAAV 299
           RA+R    R+ +F+V  I +++ ++P     L+         SPF  VF + G+  +A +
Sbjct: 242 RAIRTTVLRLAVFFVGTIFVLATLLPREQAGLVE--------SPFVTVFTYIGIPYSADI 293

Query: 300 MNAVILTAVLSAGNSGMYASTRMLYTLACDGKAPRIFAKLSRGGVPRNALYATTVIAGLC 359
           MN VI++A+LSA NSG+YA++RML+TL+  G  P+ F+ L+R G P NA+  +       
Sbjct: 294 MNFVIISALLSAANSGLYAASRMLWTLSDQGHLPKQFSALTRMGTPLNAIIVSMAGGAAS 353

Query: 360 FLTSMFGNQTVYLWLLNTSGMTGFIAWLGIAISHYRFRRGYVLQGHDINDLPYRSGFFPL 419
            L+S+F   T+YL L++ SG+   + W+ IA S   FRR YV  G DI  L +R   +P 
Sbjct: 354 LLSSVFAADTIYLALVSISGLAVVVVWMSIAASQIAFRRHYVANGGDIRKLKFRVRGYPW 413

Query: 420 GPIFAFILCLIITLGQNYEAFLKDTIDWGGVAATYIGIPLFLIIWFGYKLIKGTHFVRYS 479
            P+ A + C +  +G  ++   +         A Y G+P     +F Y + + +   R S
Sbjct: 414 VPLGALVCCSLACIGIAFDPEQR--------VALYFGLPFIAWCYFVYYITRKSRERRLS 465


Lambda     K      H
   0.327    0.142    0.451 

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: 736
Number of extensions: 46
Number of successful extensions: 3
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: 489
Length of database: 476
Length adjustment: 34
Effective length of query: 455
Effective length of database: 442
Effective search space:   201110
Effective search space used:   201110
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: 52 (24.6 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