GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK in Brucella inopinata BO1

Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate WP_008510542.1 BIBO1_RS17490 ABC transporter ATP-binding protein

Query= reanno::Smeli:SMc03065
         (362 letters)



>NCBI__GCF_000182725.1:WP_008510542.1
          Length = 333

 Score =  345 bits (884), Expect = 1e-99
 Identities = 197/366 (53%), Positives = 242/366 (66%), Gaps = 38/366 (10%)

Query: 1   MTGLLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDM 60
           M  L LK + K YGA +V+  I+L++ +GEF++FVGPSGCGKSTLLR IAGLE+++ G +
Sbjct: 1   MGSLQLKSVHKRYGAQEVLKDINLEVNDGEFIIFVGPSGCGKSTLLRSIAGLEDVSAGQV 60

Query: 61  FIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADM 120
            I+GE V   PPS+RGIAMVFQSYALYPH+TV  NM  G++ A   K+EI+ RV  A+ M
Sbjct: 61  LINGEDVTVTPPSRRGIAMVFQSYALYPHLTVKANMGLGLKQAGAPKDEIEGRVAKASAM 120

Query: 121 LQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLS 180
           L L PYL R P  LSGGQRQRVAIGRA+ RNP++FLFDEPLSNLDAALRV TR+EIAKL 
Sbjct: 121 LALEPYLARRPAELSGGQRQRVAIGRALVRNPELFLFDEPLSNLDAALRVQTRLEIAKLH 180

Query: 181 ERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAM 240
             +   TMIYVTHDQVEAMTLADRIVVL+AG IEQ+G+P+ELY RP NLFVA FIGSP M
Sbjct: 181 RELK-ATMIYVTHDQVEAMTLADRIVVLNAGRIEQIGSPMELYNRPDNLFVAGFIGSPQM 239

Query: 241 NVIPAT-ITATGQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVTEADDFLFE 299
           N I A  I ATG +T                           G+RPE L V+  +   ++
Sbjct: 240 NFIEAARIGATGART--------------------------IGIRPEHLSVSR-ESGTWK 272

Query: 300 GTVSIVEALGEVTLLYIE----GLVENEPIIAKMPGIARVGRGDKVRFTADKAKLHLFDT 355
           G V   E LG  T+LY+E    GLV      A++ G       D +  T ++ K H FD 
Sbjct: 273 GKVIHAEHLGADTILYVETETAGLV-----TARLFGEQHYNEDDVIFLTPEEGKTHYFDE 327

Query: 356 NGQSYR 361
            G++ R
Sbjct: 328 AGKAIR 333


Lambda     K      H
   0.320    0.137    0.387 

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: 356
Number of extensions: 14
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: 362
Length of database: 333
Length adjustment: 29
Effective length of query: 333
Effective length of database: 304
Effective search space:   101232
Effective search space used:   101232
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.

Links

Downloads

Related tools

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