GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21725 in Escherichia coli BW25113

Align ABC transporter for D-Glucosamine, putative ATPase component (characterized)
to candidate 17341 b3271 predicted amino-acid transporter subunit (NCBI)

Query= reanno::pseudo5_N2C3_1:AO356_00465
         (263 letters)



>FitnessBrowser__Keio:17341
          Length = 252

 Score =  244 bits (622), Expect = 2e-69
 Identities = 130/252 (51%), Positives = 168/252 (66%), Gaps = 12/252 (4%)

Query: 7   PSNTQPLLDIRGLRKQYGPLEVLKGVDLSMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQ 66
           P+N   ++ +  + K YG   VLK ++L++Q G  + L G SGSGK+T +RC+N LEE Q
Sbjct: 8   PANA--MITLENVNKWYGQFHVLKNINLTVQPGERIVLCGPSGSGKSTTIRCINHLEEHQ 65

Query: 67  GGQIVLDGESIGYDDIDGKRVRHPEKLIARHRAMTGMAFQQFNLFPHLTALQNVTLGLLK 126
            G+IV+DG  +  D  + +RVR             GM FQ FNLFPHLT LQN TL  + 
Sbjct: 66  QGRIVVDGIELNEDIRNIERVRQE----------VGMVFQHFNLFPHLTVLQNCTLAPIW 115

Query: 127 VKKLPKDEAVALAEKWLERVGLLERRDHFPGQLSGGQQQRVAIARAIAMNPSLMLFDEVT 186
           V+K+PK EA  LA  +LERV + E    FPGQ+SGGQQQRVAIAR++ M P +MLFDE T
Sbjct: 116 VRKMPKKEAEDLAVHYLERVRIAEHAHKFPGQISGGQQQRVAIARSLCMKPKIMLFDEPT 175

Query: 187 SALDPELVGEVLNVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELF 246
           SALDPE+V EVL+ + GLA+ GMTML VTHEM FA  V+D+++FM++G I EQ  P E F
Sbjct: 176 SALDPEMVKEVLDTMIGLAQSGMTMLCVTHEMGFARTVADRVIFMDRGEIVEQAAPDEFF 235

Query: 247 ERPQSPRLAEFL 258
             P+S R   FL
Sbjct: 236 AHPKSERTRAFL 247


Lambda     K      H
   0.320    0.138    0.392 

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: 203
Number of extensions: 8
Number of successful extensions: 2
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: 263
Length of database: 252
Length adjustment: 24
Effective length of query: 239
Effective length of database: 228
Effective search space:    54492
Effective search space used:    54492
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 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