GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21725 in Williamsia sterculiae CPCC 203464

Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate WP_076482473.1 BW971_RS17350 amino acid ABC transporter ATP-binding protein

Query= reanno::pseudo3_N2E3:AO353_21725
         (265 letters)



>NCBI__GCF_900156495.1:WP_076482473.1
          Length = 250

 Score =  253 bits (646), Expect = 3e-72
 Identities = 130/238 (54%), Positives = 168/238 (70%)

Query: 23  KQYGPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQILLDGESIGYH 82
           K +G L+VLKG+ L ++RG V  LIG SGSGK+T LRCVN LE    G++ +D + IGY 
Sbjct: 9   KSFGALQVLKGISLEVERGEVTCLIGPSGSGKSTFLRCVNHLESVTAGRLYVDDDLIGYR 68

Query: 83  EVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKLHKDEAVVLAE 142
           E  GK    S K  A  R   GM FQ FNLFPH TAL N+    ++VK + +  AV   +
Sbjct: 69  EKGGKLYELSAKDAAAQRRDIGMVFQHFNLFPHRTALDNIIEAPIQVKGVVRARAVERGK 128

Query: 143 KWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALDPELVGEVLSV 202
             L++VGL ++   YP QLSGGQQQRVAIARA+AM+P LMLFDE TSALDPELVG+VL+V
Sbjct: 129 DLLDQVGLADKASAYPAQLSGGQQQRVAIARALAMDPKLMLFDEPTSALDPELVGDVLAV 188

Query: 203 IKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFERPQSPRLAEFL 260
           ++ LA+DGMTM++VTHEM FA EV+D++VFM+ G++ E+G P+E+   PQ  R   FL
Sbjct: 189 MRNLAKDGMTMVVVTHEMGFAREVADQLVFMDAGKVVEKGDPREVLNSPQHERTQSFL 246


Lambda     K      H
   0.319    0.135    0.379 

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: 197
Number of extensions: 4
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: 265
Length of database: 250
Length adjustment: 24
Effective length of query: 241
Effective length of database: 226
Effective search space:    54466
Effective search space used:    54466
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 24 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