GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Pseudomonas simiae WCS417

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate GFF3451 PS417_17665 ABC transporter permease

Query= uniprot:Q1MCU0
         (300 letters)



>FitnessBrowser__WCS417:GFF3451
          Length = 286

 Score =  149 bits (377), Expect = 6e-41
 Identities = 86/296 (29%), Positives = 157/296 (53%), Gaps = 14/296 (4%)

Query: 1   MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI 60
           +  ++ Q+LNGL LG IY L+++G T+++G++  +NFAHG  F+LG +    +     S+
Sbjct: 2   LNLYLFQILNGLGLGMIYFLISVGLTIIFGLLNFVNFAHGAFFLLGAY----ICYTAVSL 57

Query: 61  FAGLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQ 120
                +A+L+  ++V A+       W IERV  + +     +  ++  +G+++ +     
Sbjct: 58  TGNFWLALLIAPLVVAALA------WVIERVLIQRIYHLPHMFQILVTLGIALIIQEASV 111

Query: 121 VTQGPRNK--PIPPMVSSVYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRA 178
           +  GP  K   +P ++  V   G+      ++ +IV + ++    W ++ RT  G   RA
Sbjct: 112 MIWGPVGKSVAVPELLRGVLVVGDFVYPYYRLFLIVFSGLVGLGLWLLLERTRFGALVRA 171

Query: 179 TEQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAA 238
             +  +  +LLG N+ +  S+TF +G ALA VAG ++    G   F      GV AF   
Sbjct: 172 GSESTETVSLLGTNIFRLFSMTFALGVALAGVAGVLFAPLRGAQPFVGPEILGV-AFVVV 230

Query: 239 VLGGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILGR 294
           V+GG+GS  GA+ GGLL+G+++SL +  +      +  +  +A V++ +P G+ GR
Sbjct: 231 VIGGMGSFSGALVGGLLVGVVQSLMTTLWPQG-ASLMIYGAMAVVILVRPYGLFGR 285


Lambda     K      H
   0.329    0.143    0.421 

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: 310
Number of extensions: 22
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: 300
Length of database: 286
Length adjustment: 26
Effective length of query: 274
Effective length of database: 260
Effective search space:    71240
Effective search space used:    71240
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 (21.8 bits)
S2: 48 (23.1 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