GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztB in Pseudomonas fluorescens FW300-N2E3

Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate AO353_04610 AO353_04610 amino acid ABC transporter permease

Query= CharProtDB::CH_011913
         (426 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_04610
          Length = 393

 Score =  306 bits (783), Expect = 9e-88
 Identities = 182/421 (43%), Positives = 254/421 (60%), Gaps = 37/421 (8%)

Query: 8   PKAGFRLSMLIYDTRFRSITIQIVVLLLFLAGLVWLLNNAYVNLEAKGKDFNFSFLWTRA 67
           PK    LS    D R R+   QI+ ++  ++   +L NN   NL+ +G    FSFL   A
Sbjct: 8   PKQRLSLS----DPRVRAWLFQIITIVAVISMGWYLFNNTQTNLQHRGITSGFSFLERSA 63

Query: 68  GYDLAQTLIPYSNDDTHFRALIEGLLNTLLVSVLGCILATILGTIIGVLRLSQNWLVARI 127
           G+ +AQ LI Y+  D++ R  + GLLNTLLV+ +G ILATILG I+GV RLS+NW++ ++
Sbjct: 64  GFGIAQHLIDYTESDSYARVFVIGLLNTLLVTFIGVILATILGFIVGVARLSKNWIINKL 123

Query: 128 MTVYVETFRNIPLLLWILLMGTILAETRPVPKDFRLTEAMKAAGEEPKASMWFFDSVAVT 187
            TVYVETFRNIP LL IL     +  T P P++                S  F D+  V+
Sbjct: 124 ATVYVETFRNIPPLLQILFWYFAVFLTMPGPRN----------------SHNFADTFFVS 167

Query: 188 NRGTNLPAPAFDHSLGVVDLGWNLPVSLNALAILAVMSASFWGWRRFMARAKAVQEATGT 247
           +RG N+PA    +        W   +S+  +AI+A++    W  +RF        EATG 
Sbjct: 168 SRGLNMPAAQMANGF------WAFVISI-VVAIVAIVLMCRWANKRF--------EATGV 212

Query: 248 RPTTWWP--SLLILFAPISALLYGLGFHLDYPQITKFDFTGGFQMLHSFTALLIALTLYT 305
               +W   +L +L   + AL++G+  H + P++  F+F GG+ ++    AL +ALT+YT
Sbjct: 213 PFHKFWVGLALFLLIPALCALIFGVPLHWEMPKLQGFNFVGGWVLIPELLALTLALTVYT 272

Query: 306 AAFIAEIVRAGIQAISRGQTEAAYALGLRPGRTMSLVILPQALRVIVPPLISQFLNLTKN 365
           AAFIAEIVR+GI ++S GQTEAA +LGLR G T+  VI+PQALRVI+PPL SQ+LNL KN
Sbjct: 273 AAFIAEIVRSGINSVSHGQTEAARSLGLRNGPTLRKVIIPQALRVIIPPLTSQYLNLAKN 332

Query: 366 SSLAIAVSYMDLRGTLGGITLNQTGRELECMLLMMLIYLTISLTISSLMNLYNKSIKLKE 425
           SSLA  + Y ++     G  LNQTG+ +E + + M +YL IS++IS LMN YNK I L E
Sbjct: 333 SSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLAISISISLLMNWYNKRIALIE 392

Query: 426 R 426
           R
Sbjct: 393 R 393


Lambda     K      H
   0.326    0.139    0.419 

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: 381
Number of extensions: 12
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: 426
Length of database: 393
Length adjustment: 31
Effective length of query: 395
Effective length of database: 362
Effective search space:   142990
Effective search space used:   142990
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: 50 (23.9 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