GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braE in Pseudomonas fluorescens FW300-N2C3

Align High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate AO356_28380 AO356_28380 ABC transporter permease

Query= TCDB::P21628
         (417 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_28380
          Length = 355

 Score =  131 bits (330), Expect = 3e-35
 Identities = 103/334 (30%), Positives = 156/334 (46%), Gaps = 42/334 (12%)

Query: 92  RWAVLALVVVAFVWPFFASRGAVDIATLI--LIYVMLGIGLNIVVGLAGLLDLGYVGFYA 149
           R  + AL++ AFV   +        A LI  L+  + G+GLN++ G AG L LG   F A
Sbjct: 26  RHGLAALLLFAFVVVPWLGNDYWFSAILIPFLVLSLAGLGLNLLTGYAGQLSLGSAAFMA 85

Query: 150 VGAY-TYALLAEYAGFGFWTALPIAGMMAALFGFLLGFPVLRLRGDYLAIVTLGFGEIIR 208
           VGA+ TY L    AG     ++ + G+ AAL   L G P LR++G YL + TL     + 
Sbjct: 86  VGAFATYNLEIRVAGLPLLVSIALGGLTAALVAVLFGLPSLRIKGFYLLVSTLAAQFFVT 145

Query: 209 ILLRNMTEITGGP-NGIGSIPKPTLFGLTFERRAPEGMQTFHEFFGIAYNTNYKVILLYV 267
             L   +  +    +G+ S P+  +FG+  +  AP G                     Y+
Sbjct: 146 WALTRFSWFSNNSASGVISAPRLDVFGVNLD--APAGR--------------------YL 183

Query: 268 VALLLVLLALFVINRLMRMPIGRAWEALREDEVACRALGLNPTIVKLSAFTIGASFAGFA 327
           + L +V+   ++   L+R  +GR W A+R+ + A   +G+     KL AF I   F G A
Sbjct: 184 LTLSVVVALFWLGKNLVRSELGRNWMAVRDMDTAAAVIGIALAKTKLLAFAISGFFLGVA 243

Query: 328 GSFFA-ARQGLVTPESFTFIESAMILAIVVLGGMGSQLGVILAAVVMVL----------- 375
           G+ +A A  G V P  F    S  IL I+++GG+GS LG  L A  +VL           
Sbjct: 244 GALWAFAYLGTVEPHGFDLNRSFQILFIIIIGGLGSLLGNFLGAAFIVLFPVLLSNLVSL 303

Query: 376 ----LQEMRGFNEYRMLIFGLTMIVMMIWRPQGL 405
               L +       + +IFG  +I+ +I  P+GL
Sbjct: 304 LPGGLVDAGQVENLQKMIFGALIILFLIKEPEGL 337


Lambda     K      H
   0.330    0.146    0.439 

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: 354
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: 417
Length of database: 355
Length adjustment: 30
Effective length of query: 387
Effective length of database: 325
Effective search space:   125775
Effective search space used:   125775
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 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