GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gntC in Escherichia coli BW25113

Align D-gluconate TRAP transporter, periplasmic component (characterized)
to candidate 17640 b3579 predicted transporter (NCBI)

Query= reanno::psRCH2:GFF2082
         (338 letters)



>FitnessBrowser__Keio:17640
          Length = 328

 Score =  208 bits (530), Expect = 1e-58
 Identities = 112/315 (35%), Positives = 184/315 (58%), Gaps = 13/315 (4%)

Query: 23  AQAADDIRPRMIRFGYGLNEDSNQGRAAKLLAEEVAKASGGKLKVRTFASASLGSDDQMQ 82
           A +   +  + +RFGY  ++  +Q  AAK   + + + + G+LK++ F  ++LG+   M 
Sbjct: 17  AFSTSSLAAQSLRFGYETSQTDSQHIAAKKFNDLLQERTKGELKLKLFPDSTLGNAQAMI 76

Query: 83  NALIGGAQEMMVGSTATLVGISKEMAVWDTPFLFTDPRQADQVLDGPVGRQVMDKLEEKG 142
           + + GG  +M +  +    G+S  M + D PFLF D   A + LDG VG  +   LE KG
Sbjct: 77  SGVRGGTIDMEMSGSNNFAGLSPVMNLLDVPFLFRDTAHAHKTLDGKVGDDLKASLEGKG 136

Query: 143 LVGLVYWENGFRNVTNSARPIEKLEDFNGVKLRVMPNPVFIDTFKRMGANAVPLPFSELF 202
           L  L YWENG+R+VTNS  P++   D  G+K+R   +P+ I  FK  GAN +P+PF+E++
Sbjct: 137 LKVLAYWENGWRDVTNSRAPVKTPADLKGLKIRTNNSPMNIAAFKVFGANPIPMPFAEVY 196

Query: 203 TALETKAVDGQENPFNTILSSKFYEVQKYLSVTNHVYSPWIVTVSKRWWDGLSATEQGIL 262
           T LET+ +D QE+P N + S+KF+EVQK+LS+T+H YSP +V ++K  +DGLS   Q  L
Sbjct: 197 TGLETRTIDAQEHPINVVWSAKFFEVQKFLSLTHHAYSPLLVVINKAKFDGLSPEFQQAL 256

Query: 263 MEAAEKARDAEREDTRREASQALAALKERGMQINEVSPDEIQRMREKAQPAIQTVIDAVG 322
           + +A++A + +R+    +  + +  +KE G+++       I  +  KA        DA+G
Sbjct: 257 VSSAQEAGNYQRKLVAEDQQKIIDGMKEAGVEV-------ITDLDRKA------FSDALG 303

Query: 323 QELFDQVQAEVEKAA 337
            ++ D    +V + A
Sbjct: 304 NQVRDMFVKDVPQGA 318


Lambda     K      H
   0.315    0.131    0.368 

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: 236
Number of extensions: 8
Number of successful extensions: 1
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: 338
Length of database: 328
Length adjustment: 28
Effective length of query: 310
Effective length of database: 300
Effective search space:    93000
Effective search space used:    93000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 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