GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1695 in Pseudomonas fluorescens GW456-L13

Align ABC transporter permease (characterized, see rationale)
to candidate PfGW456L13_123 High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1)

Query= uniprot:A0A165KC95
         (309 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_123
          Length = 304

 Score =  265 bits (676), Expect = 1e-75
 Identities = 146/310 (47%), Positives = 207/310 (66%), Gaps = 14/310 (4%)

Query: 3   ILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMP 62
           I LQQ++NGL LGS+Y LIA+GYTMVYGII +INFAHGEV MI A  +   + ++  A  
Sbjct: 4   IFLQQLVNGLTLGSVYGLIAIGYTMVYGIIGMINFAHGEVYMISAYLAAISLALL--AYF 61

Query: 63  GAPGWVILLLATII-ACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAMI 121
           G   + +L+L T+I   VV A   +VIE+VAY+PLR+S RLAPLI+AIG+S++LQ  A I
Sbjct: 62  GIESFPLLMLGTLIFTIVVTAVYGWVIERVAYKPLRNSTRLAPLISAIGISLILQNYAQI 121

Query: 122 IWKPNYKPYPTMLPSS-PFEIGGAFI--TPTQILILGVTAVALASLVYLVNHTNLGRAMR 178
                 +  PT+L  +   +IG  F+  T T++ IL    V +  L Y++ +T LGR  R
Sbjct: 122 SQGAKQQGVPTLLSGAWRVDIGTGFVQLTYTKVFILVAAFVGMGLLTYVIKYTKLGRMCR 181

Query: 179 ATAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTA 238
           AT ++ ++AS++G+  D VIS  FIIGA +AA+AG++   NYGT     GF+ G+KAFTA
Sbjct: 182 ATQQDRKMASILGINTDRVISYVFIIGAAMAALAGVLITMNYGTFDFYAGFIIGIKAFTA 241

Query: 239 AVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPS 298
           AV GGIG+L GA++GGI+LG+ E++ S        GL+ S Y D+F+F +L+++L  RP 
Sbjct: 242 AVLGGIGSLPGAMLGGIILGISESLFS--------GLVNSDYKDVFSFSLLVLVLVFRPQ 293

Query: 299 GLLGERVADR 308
           GLLG  +  +
Sbjct: 294 GLLGRPLVSK 303


Lambda     K      H
   0.327    0.142    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: 283
Number of extensions: 8
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: 309
Length of database: 304
Length adjustment: 27
Effective length of query: 282
Effective length of database: 277
Effective search space:    78114
Effective search space used:    78114
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: 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