GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1B in Synechococcus elongatus PCC 7942

Align PEP1B, component of Uptake system for glutamate and aspartate (characterized)
to candidate Synpcc7942_0248 Synpcc7942_0248 Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine

Query= TCDB::A1VZQ3
         (250 letters)



>FitnessBrowser__SynE:Synpcc7942_0248
          Length = 396

 Score =  125 bits (314), Expect = 1e-33
 Identities = 76/242 (31%), Positives = 132/242 (54%), Gaps = 14/242 (5%)

Query: 11  LRQILTSWGLYDENSISPFAVWKFLDALDNKDAFIN---GFIYTLEVSILALLIATIFGT 67
           LR + T WG+     +    +W     L  +    N   G + TL  ++++++ +   G 
Sbjct: 156 LRFLPTLWGV-----LFLVGLWLLQGGLGLRPVSSNDWSGLLLTLATALISMVCSLPLGI 210

Query: 68  IGGVMATSRFKIIRAYTRIYVELFQNVPLVIQIFFLFYALPVL---GIRLDIFTIGVLGV 124
           +  +   S    IR  +  Y+ELF+ +PLV  +FF    +P++     R+D     ++G+
Sbjct: 211 LLALGRQSSLPAIRWLSVTYIELFRGLPLVTILFFGQVMVPLMLDSEWRIDRILRAIVGL 270

Query: 125 GAYHGAYVSEVVRSGILAVPRGQFEASASQGFTYIQQMRYIIVPQTIRIILPPMTNQMVN 184
             +  AY++E VR G+ A+P+GQFEA+A+ G    Q  R+I++PQ +RI +P +    +N
Sbjct: 271 TIFLSAYLAETVRGGLQAIPQGQFEAAAALGLNLFQTYRFIVLPQALRISIPAIVGLFLN 330

Query: 185 LIKNTSVLLIVGGAELMHSADSYAAD---YGNYAPAYIFAAVLYFIICYPLAYFAKAYEN 241
           L+++T++L IVG  EL+  + S  A+    G YA  Y+F  VLY++ CY LA  ++  E 
Sbjct: 331 LLQDTTLLSIVGLLELLGISRSILANPAYLGRYAEVYLFLGVLYWLCCYGLAQLSRRLEQ 390

Query: 242 KL 243
           +L
Sbjct: 391 RL 392


Lambda     K      H
   0.328    0.143    0.422 

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: 249
Number of extensions: 13
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: 250
Length of database: 396
Length adjustment: 27
Effective length of query: 223
Effective length of database: 369
Effective search space:    82287
Effective search space used:    82287
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.

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