GapMind for catabolism of small carbon sources

 

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

Align tryptophan permease (characterized)
to candidate Pf6N2E2_4959 S-methylmethionine permease

Query= CharProtDB::CH_091156
         (592 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4959
          Length = 476

 Score =  214 bits (546), Expect = 5e-60
 Identities = 144/463 (31%), Positives = 227/463 (49%), Gaps = 20/463 (4%)

Query: 76  SNLKRTLKPRHLIMIAIGGSIGTGLFVGSGKAIAEGGPLGVVIGWAIAGSQIIGTIHGLG 135
           +  K+ ++ RH++M+A+GG IGTGLF+ SG  + + GP+G VI + I    +   +  LG
Sbjct: 12  AGFKQEMQTRHIVMLALGGVIGTGLFLTSGYTVNQAGPMGAVIAYIIGALMVYMVMMCLG 71

Query: 136 EITVRFPVVGAFANYGTRFLDPSISFVVSTIYVLQWFFVLPLEIIAAAMTVQYWNSSIDP 195
           E+ V+ P  G+F+ Y TRFL P   + V+ +Y L W   +  E  AA + +  W      
Sbjct: 72  ELAVQMPETGSFSTYATRFLGPGTGYTVAWLYWLTWTVAIGSEFTAAGILMSRWFPDTPV 131

Query: 196 VIWVAIFYAVIVSINLFGVRGFGEAEFAFSTIKAITVCGFIILCVVLICG--GGPDHEFI 253
            IW A+F  V+   N+  VR F E EF  S IK +TV  F+++    I G         I
Sbjct: 132 WIWSALFAGVVFLSNVISVRLFAETEFWLSLIKVLTVVVFLLIGGGAILGLLNIDQAHSI 191

Query: 254 GAKYWHDPGCLANGFPGVLSVLVVASYSLGGIEMTCLASGET-DP-KGLPSAIKQVFWRI 311
           G   +   G    GF  +   L+  S++  G E+  +A+GET DP + +P AI+    R+
Sbjct: 192 GLSNFTREGLFPTGFMPIAMTLLAVSFAFSGTELIGIAAGETKDPQRNVPRAIRTTVLRL 251

Query: 312 LFFFLISLTLVGFLVPYTNQNLLGGSSVDNSPFVIAIKLHHIKALPSIVNAVILISVLSV 371
             FF+ ++ ++  L+P     L+       SPFV       I     I+N VI+ ++LS 
Sbjct: 252 AVFFVGTIFVLATLLPREQAGLV------ESPFVTVFTYIGIPYSADIMNFVIISALLSA 305

Query: 372 GNSCIFASSRTLCSMAHQGLIPWWFGYIDRAGRPLVGIMANSLFGLLAFLVKSGSMSEVF 431
            NS ++A+SR L +++ QG +P  F  + R G PL  I+ +   G  + L    +   ++
Sbjct: 306 ANSGLYAASRMLWTLSDQGHLPKQFSALTRMGTPLNAIIVSMAGGAASLLSSVFAADTIY 365

Query: 432 NWLMAIAGLATCIVWLSINLSHIRFRLAMKAQGKSLDELEFVSAVGIWGSAYSALINCLI 491
             L++I+GLA  +VW+SI  S I FR    A G  + +L+F      W          + 
Sbjct: 366 LALVSISGLAVVVVWMSIAASQIAFRRHYVANGGDIRKLKFRVRGYPW----------VP 415

Query: 492 LIAQFYCSLWPIGGWTSGKERAKIFFQNYLCALIMLFIFIVHK 534
           L A   CSL  IG     ++R  ++F     A      +I  K
Sbjct: 416 LGALVCCSLACIGIAFDPEQRVALYFGLPFIAWCYFVYYITRK 458


Lambda     K      H
   0.326    0.141    0.447 

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: 701
Number of extensions: 35
Number of successful extensions: 4
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: 592
Length of database: 476
Length adjustment: 35
Effective length of query: 557
Effective length of database: 441
Effective search space:   245637
Effective search space used:   245637
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 (21.6 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