GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21725 in Methanospirillum stamsii Pt1

Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate WP_109939631.1 DLD82_RS02995 ATP-binding cassette domain-containing protein

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



>NCBI__GCF_003173335.1:WP_109939631.1
          Length = 378

 Score =  132 bits (333), Expect = 8e-36
 Identities = 91/249 (36%), Positives = 137/249 (55%), Gaps = 23/249 (9%)

Query: 16  LEIRDLHKQYGPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQILLD 75
           L++  + K Y     +  + L++Q G ++TLIG SGSGKTT L+ +N L E   G+IL++
Sbjct: 18  LDLTGVSKWYNNSCAVSYLTLSIQGGELITLIGGSGSGKTTTLKMINRLIEPDSGEILIN 77

Query: 76  GESIGYHEVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKLHKD 135
           G++  +   N   +R S           G   QQ  LFPH++  +N+++ L  + K+H+D
Sbjct: 78  GQN--FLSFNPVALRRS----------IGYVIQQIGLFPHMSVAENISIPLT-LGKVHQD 124

Query: 136 EAVVLAEKWLERVGLLER--RDHYPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALDP 193
                 ++ L  V L     RD  P +LSGGQQQRV +ARA+A +P L+L DE   ALDP
Sbjct: 125 RIRNRIDELLTLVSLSPDTFRDRKPSELSGGQQQRVGLARALAADPPLLLMDEPFGALDP 184

Query: 194 ----ELVGEVLSVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFE 249
               +L  E L + K L   G T++ VTH++  AF +SD+I  + +G +     P EL  
Sbjct: 185 LLRRQLQEEFLRIKKSL---GKTIIFVTHDIDEAFLLSDRIAVLREGSLHALTTPPELLV 241

Query: 250 RPQS-PRLA 257
             Q+ P LA
Sbjct: 242 AAQNDPYLA 250


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: 226
Number of extensions: 10
Number of successful extensions: 4
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: 378
Length adjustment: 27
Effective length of query: 238
Effective length of database: 351
Effective search space:    83538
Effective search space used:    83538
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: 48 (23.1 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