GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1695 in Synechococcus elongatus PCC 7942

Align ABC transporter permease (characterized, see rationale)
to candidate Synpcc7942_2177 Synpcc7942_2177 integral membrane protein of the ABC-type Nat permease for neutral amino acids NatD

Query= uniprot:A0A165KC95
         (309 letters)



>FitnessBrowser__SynE:Synpcc7942_2177
          Length = 296

 Score =  144 bits (362), Expect = 3e-39
 Identities = 100/302 (33%), Positives = 157/302 (51%), Gaps = 28/302 (9%)

Query: 4   LLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMPG 63
           L Q  INGL  GS+ AL A G T++YGI++L NFA GE L +GA  +     +      G
Sbjct: 15  LAQLAINGLATGSLLALAATGLTLIYGILRLTNFAQGEFLTLGAYFTLVANSL------G 68

Query: 64  APGWVIL---LLATIIACVVAATLNFVIEKVAYRPLRSS--PRLAPLITAIGMSILLQTL 118
              W+ +    +ATI  C++        E V + PLR         +I  IG+S+ L+ L
Sbjct: 69  LSLWLAIPLGAIATIALCLLG-------EAVLWEPLRRQRVNTTTLIILTIGLSLFLRNL 121

Query: 119 AMIIWKPNYKPYPTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMR 178
            ++IW    + Y  +       + G  IT   +L++   A AL  L +++  T++G+ MR
Sbjct: 122 VILIWGAGNQAY-RLAVQPALTLWGLRITLNSLLVVIGAAAALVLLHWVLQRTSIGKGMR 180

Query: 179 ATAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTA 238
           A A++P +A + GV  + VI  T++I   L AIAG +Y       + TMG+   L  F +
Sbjct: 181 AIADDPDLARVSGVPVETVIRWTWVIAGGLTAIAGGLYGL-ITAVRPTMGWNLILPLFAS 239

Query: 239 AVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPS 298
           A+ GGIG+  GA+ GG++LG  + + + +        L + Y    AF++LI +L +RP 
Sbjct: 240 AILGGIGSPYGAIAGGLILGFAQELSTYW--------LPAEYKLAVAFVILIGVLVIRPQ 291

Query: 299 GL 300
           GL
Sbjct: 292 GL 293


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: 239
Number of extensions: 17
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: 309
Length of database: 296
Length adjustment: 27
Effective length of query: 282
Effective length of database: 269
Effective search space:    75858
Effective search space used:    75858
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