GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21725 in Klebsiella michiganensis M5al

Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate BWI76_RS10370 BWI76_RS10370 ABC transporter-like protein

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



>FitnessBrowser__Koxy:BWI76_RS10370
          Length = 259

 Score =  254 bits (650), Expect = 1e-72
 Identities = 127/248 (51%), Positives = 176/248 (70%), Gaps = 1/248 (0%)

Query: 13  QALLEIRDLHKQYGPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQI 72
           + ++ IR LHK++G   VL+G+DL +  G  + +IG SGSGK+TLLRC+N +E    G +
Sbjct: 5   KVVMRIRALHKRFGAQSVLQGIDLDIYAGEKIAIIGGSGSGKSTLLRCLNFMEIPSAGTV 64

Query: 73  LLDGESIGYHEVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKL 132
            LDG ++G  +  G+R R+SEK ++  R   GM FQQFNLFPHLT LQNV+  L+ VKK+
Sbjct: 65  ELDGVTLGKIDSRGQR-RYSEKQLSDVRQRVGMVFQQFNLFPHLTVLQNVSEALISVKKM 123

Query: 133 HKDEAVVLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALD 192
            ++EA+ +A   LE+VGL  +   +PG LSGGQQQRVAIARA+AM P ++LFDE TS+LD
Sbjct: 124 RREEAMRIARAQLEKVGLGHKHQAWPGSLSGGQQQRVAIARALAMTPEIILFDEPTSSLD 183

Query: 193 PELVGEVLSVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFERPQ 252
           PELVGEVL  I+ LA++G T+LLVTHE+ FA+  +D+++F+  G I E G  +E+   P+
Sbjct: 184 PELVGEVLHTIRELADEGRTLLLVTHELGFAWHFADRVIFIENGVIHEMGTAEEVLRHPR 243

Query: 253 SPRLAEFL 260
            PR   FL
Sbjct: 244 QPRTQAFL 251


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: 10
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: 259
Length adjustment: 25
Effective length of query: 240
Effective length of database: 234
Effective search space:    56160
Effective search space used:    56160
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