GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PfGW456L13_1895 in Synechococcus elongatus PCC 7942

Align ABC transporter for D-Galactose and D-Glucose, permease component 1 (characterized)
to candidate Synpcc7942_0526 Synpcc7942_0526 ABC-type sugar transport systems permease components-like

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1895
         (302 letters)



>FitnessBrowser__SynE:Synpcc7942_0526
          Length = 293

 Score =  123 bits (308), Expect = 6e-33
 Identities = 78/273 (28%), Positives = 139/273 (50%), Gaps = 3/273 (1%)

Query: 18  RWLPKLVLAPSMLIVLVGFYGYIIWTFILSFTNSSF--MPSYKWVGLQQYMRLMDNDRWW 75
           R  P L LAP++ I+ +  +   +  F  SFT   +    S +WVGL+ + RL+++  +W
Sbjct: 7   RLSPYLFLAPALTILGLTVFWPALQAFYFSFTRFDYNLTRSPQWVGLENFQRLLNDAVFW 66

Query: 76  VASKNLALFGGMFISISLVLGVFLAVLLDQRIRKEGFIRTVYLYPMALSMIVTGTAWKWL 135
               N  ++    + + + L + LA+L+++ +R     R  Y  P+ +S++V G AW+WL
Sbjct: 67  KTLGNTFIYLIGVVPLLVFLPLGLAILVNRPLRGITLFRLAYYTPVIVSIVVAGIAWRWL 126

Query: 136 LNPGLGLDKMLRDWGWEGFR-LDWLVDQDRVVYCLVIAAVWQASGFVMAMFLAGLRGVDQ 194
                 L+++ +    EGF+ + WL      ++ ++   VW+  G+ M ++LAGL+G+  
Sbjct: 127 YAETGLLNQLGQLVFGEGFQPIPWLTSPALALFSVMAVTVWKGLGYYMVIYLAGLQGIPL 186

Query: 195 SIIRAAQVDGASLPTIYLKIVLPSLRPVFFSAFMILAHIAIKSFDLVAAMTAGGPGYSSD 254
            +  AA +DG+     +L I LP +RP      +I A  A K F+ V  MT GGP  SS 
Sbjct: 187 ELYEAAALDGSDGWRRHLDITLPLMRPYLVLVAVISAISATKVFEEVFIMTQGGPLNSSK 246

Query: 255 LPAMFMYSFTFSRGQMGIGSASAMLMLGAVLTI 287
               ++Y   F + ++       + +   VLT+
Sbjct: 247 TVVYYVYQQAFQKLEVSYACTVGLALFLVVLTL 279


Lambda     K      H
   0.329    0.141    0.448 

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: 284
Number of extensions: 25
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: 302
Length of database: 293
Length adjustment: 26
Effective length of query: 276
Effective length of database: 267
Effective search space:    73692
Effective search space used:    73692
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