GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglG' in Synechococcus elongatus PCC 7942

Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate Synpcc7942_0471 Synpcc7942_0471 ABC-type sugar transport system permease component-like

Query= uniprot:A8LLL4
         (385 letters)



>FitnessBrowser__SynE:Synpcc7942_0471
          Length = 276

 Score =  113 bits (283), Expect = 6e-30
 Identities = 72/238 (30%), Positives = 119/238 (50%), Gaps = 13/238 (5%)

Query: 153 PPEF-----TFANYENMLLDPNNSEGMARAFFNTLTVTIPATIIPILVAAFAAYALAWME 207
           PP+F     T  N+  +  +      + + F N+  V +    + +L  + AAY LA +E
Sbjct: 46  PPQFLPTQPTLDNFRRVWTE----NPLGQYFLNSTWVALLTVGLNLLFCSLAAYPLARLE 101

Query: 208 FPGRALLIALIVGLLVVPLQLALIPLLTLHNAIGIGKGYLGTWLAHTGFGMPLAIYLLRN 267
           F GR  L  LIV  +++P Q+ +IPL  L   +G+   YLG  L          I+LLR 
Sbjct: 102 FKGRQTLFLLIVATILIPFQVVMIPLYVLIINLGLRNTYLG--LVFPYLASAFGIFLLRQ 159

Query: 268 YMVGLPRDIIENAKVDGATDFQIFTKIVLPLSFPALASFAIFQFLWTWNDLLVAKVFLID 327
              G+P+D+ E A++DG  D  ++  +++P + PAL + AIF F+ +W+D L   + L +
Sbjct: 160 AFQGIPKDLEEAARIDGCNDLGVWWNVMIPSARPALITLAIFVFIGSWSDFLWPLIILDE 219

Query: 328 ATGQTTVMTNQIVELLGTRGGNWEILATAAFVSIAVPLLVFFSMQRFLVRGLLAGSVK 385
               T  +   I  L      +W ++A  + +SI     VF ++QR++V    A  VK
Sbjct: 220 PDRYTLPL--GIATLASGFSLDWRLVAAGSVLSILPVFGVFLALQRYIVPSAAASGVK 275


Lambda     K      H
   0.323    0.138    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: 286
Number of extensions: 20
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: 385
Length of database: 276
Length adjustment: 28
Effective length of query: 357
Effective length of database: 248
Effective search space:    88536
Effective search space used:    88536
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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