GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21725 in Cereibacter sphaeroides ATCC 17029

Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate WP_172599875.1 RSPH17029_RS02015 amino acid ABC transporter ATP-binding protein

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



>NCBI__GCF_000015985.1:WP_172599875.1
          Length = 249

 Score =  233 bits (595), Expect = 2e-66
 Identities = 123/252 (48%), Positives = 171/252 (67%), Gaps = 10/252 (3%)

Query: 9   QNASQALLEIRDLHKQYGPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQ 68
           Q + +  ++I  ++K YG   VL+ V++T+ +G  + + G SGSGK+TL+RC+N LEE Q
Sbjct: 2   QVSDEVAIQISQMNKWYGSFHVLRDVNMTVHKGERIVICGPSGSGKSTLIRCINRLEEHQ 61

Query: 69  GGQILLDGESIGYHEVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQNVTLGLLK 128
            GQI++DG  +         +++ +KV    R+  GM FQ FNLFPHLT L+N TL  + 
Sbjct: 62  SGQIVVDGIELT------SDLKNIDKV----RSEVGMVFQHFNLFPHLTILENCTLAPIW 111

Query: 129 VKKLHKDEAVVLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPSLMLFDEVT 188
           V+K  K EA  +A  +L++V + E+   YPGQLSGGQQQRVAIAR++ M P +MLFDE T
Sbjct: 112 VRKTPKKEAEEVAMHYLKKVKIPEQAHKYPGQLSGGQQQRVAIARSLCMKPRIMLFDEPT 171

Query: 189 SALDPELVGEVLSVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELF 248
           SALDPE++ EVL  +  LAE+GMTML VTHEM FA  V+++++FM+QG+I EQ  P E F
Sbjct: 172 SALDPEMIKEVLDTMIELAEEGMTMLCVTHEMGFAQAVANRVIFMDQGQIVEQNEPGEFF 231

Query: 249 ERPQSPRLAEFL 260
             P+S R   FL
Sbjct: 232 RNPKSERTKLFL 243


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: 194
Number of extensions: 5
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: 265
Length of database: 249
Length adjustment: 24
Effective length of query: 241
Effective length of database: 225
Effective search space:    54225
Effective search space used:    54225
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 Apr 09 2024. 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