GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Brucella inopinata BO1

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate WP_008509836.1 BIBO1_RS16200 ABC transporter ATP-binding protein

Query= reanno::Smeli:SMc02869
         (352 letters)



>NCBI__GCF_000182725.1:WP_008509836.1
          Length = 333

 Score =  386 bits (992), Expect = e-112
 Identities = 193/333 (57%), Positives = 248/333 (74%), Gaps = 1/333 (0%)

Query: 17  VGSLQLKTIRKAFGSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGSV 76
           +  LQL+ +RK+FGS EV+KG+D+D++ GEF++FVGPSGCGKSTLLR IAGLE+ TSG++
Sbjct: 1   MAELQLRDVRKSFGSFEVIKGVDMDIRPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTL 60

Query: 77  QIDGVEVGHVAPAKRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAAGM 136
            I+G  V +  P++RGIAMVFQSYALYPH+TV +NM  G++ A   + E + ++  AA M
Sbjct: 61  SINGAVVNNFNPSRRGIAMVFQSYALYPHMTVYENMAFGMQLASKSRQECKARIHAAAEM 120

Query: 137 LSLEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIARLH 196
           L L PYL R P +LSGGQRQRVAIGRAIVR+PK+FLFDEPLSNLDAALRV TRLEIARLH
Sbjct: 121 LQLTPYLERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIARLH 180

Query: 197 RSLK-ATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFIGSPQM 255
           +S++  TMIYVTHDQVEAMTLAD+I VL  GR+EQ+G+P+ELY +P +LFVAGFIGSP+M
Sbjct: 181 QSMEDTTMIYVTHDQVEAMTLADRICVLRDGRVEQIGTPLELYEKPNSLFVAGFIGSPKM 240

Query: 256 NFIEAAKLGDGEAKTIGIRPEHIGLSRESGDWKGKVIHVEHLGADTIIYIESETVGLLTV 315
           NF+         A T+G+R EH+ +  E G W G+V+H E LG+DT +YI+      L V
Sbjct: 241 NFLTGPHAEPFGAHTVGLRSEHLAIVPERGHWSGQVVHTEILGSDTYVYIDLGLEEPLVV 300

Query: 316 RLFGEHRYATDDIVHATPVIGSMHRFDADGRVI 348
           R  G       + +  +P    +HRFD  GR +
Sbjct: 301 RESGVSARKPGEALSISPTGDHVHRFDEKGRAV 333


Lambda     K      H
   0.320    0.137    0.393 

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: 390
Number of extensions: 14
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: 352
Length of database: 333
Length adjustment: 29
Effective length of query: 323
Effective length of database: 304
Effective search space:    98192
Effective search space used:    98192
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: 49 (23.5 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