GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Brucella inopinata BO1

Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate WP_008510542.1 BIBO1_RS17490 ABC transporter ATP-binding protein

Query= reanno::WCS417:GFF4321
         (386 letters)



>NCBI__GCF_000182725.1:WP_008510542.1
          Length = 333

 Score =  277 bits (709), Expect = 3e-79
 Identities = 147/323 (45%), Positives = 209/323 (64%), Gaps = 33/323 (10%)

Query: 1   MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60
           M +L+L++V+K YGA   + LK+I L + +GEF+I VGPSGCGKSTL+  IAGLE ++ G
Sbjct: 1   MGSLQLKSVHKRYGA--QEVLKDINLEVNDGEFIIFVGPSGCGKSTLLRSIAGLEDVSAG 58

Query: 61  AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120
            ++I  +DV+   P  R IAMVFQSYALYP ++V+ N+  GLK    P+ +I+  VA+ +
Sbjct: 59  QVLINGEDVTVTPPSRRGIAMVFQSYALYPHLTVKANMGLGLKQAGAPKDEIEGRVAKAS 118

Query: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180
            +L +E  L R+P +LSGGQ+QRVA+GRAL R P+++LFDEPLSNLDA LRV+ R E+  
Sbjct: 119 AMLALEPYLARRPAELSGGQRQRVAIGRALVRNPELFLFDEPLSNLDAALRVQTRLEIAK 178

Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240
           +H+ LK T +YVTHDQ+EAMTL D++ V+  G I+Q G+P E+YN P N FVA FIGSP 
Sbjct: 179 LHRELKATMIYVTHDQVEAMTLADRIVVLNAGRIEQIGSPMELYNRPDNLFVAGFIGSPQ 238

Query: 241 MNFVPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGEGDS 300
           MNF+            A + +  AR                  +G+RPE + ++   G  
Sbjct: 239 MNFIE----------AARIGATGAR-----------------TIGIRPEHLSVSRESG-- 269

Query: 301 ASSIRAEVQVTEPTGPDTLVFVQ 323
             + + +V   E  G DT+++V+
Sbjct: 270 --TWKGKVIHAEHLGADTILYVE 290


Lambda     K      H
   0.318    0.135    0.382 

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: 347
Number of extensions: 16
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: 386
Length of database: 333
Length adjustment: 29
Effective length of query: 357
Effective length of database: 304
Effective search space:   108528
Effective search space used:   108528
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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