GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc04256 in Brucella inopinata BO1

Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate WP_008509836.1 BIBO1_RS16200 ABC transporter ATP-binding protein

Query= reanno::Smeli:SMc04256
         (361 letters)



>NCBI__GCF_000182725.1:WP_008509836.1
          Length = 333

 Score =  276 bits (706), Expect = 6e-79
 Identities = 159/350 (45%), Positives = 217/350 (62%), Gaps = 39/350 (11%)

Query: 1   MTSVSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQI 60
           M  + +RD+  +FG+  V+  +++DI  GEF+V +G SGCGKSTLL  IAGL +++ G +
Sbjct: 1   MAELQLRDVRKSFGSFEVIKGVDMDIRPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTL 60

Query: 61  FIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEI 120
            I    V    P  RGI MVFQSYALYP MTV +N++FG+++A     E + R+  A+E+
Sbjct: 61  SINGAVVNNFNPSRRGIAMVFQSYALYPHMTVYENMAFGMQLASKSRQECKARIHAAAEM 120

Query: 121 LQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLH 180
           LQ+ P L+R P +LSGGQRQRVAIGRA+VRD  VFLFDEPLSNLDA LR   R+EI RLH
Sbjct: 121 LQLTPYLERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIARLH 180

Query: 181 QSLKN-TMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSM 239
           QS+++ TMIYVTHDQ+EA+TLADRI V++ G ++Q+  P+ +Y  P +LFVAGFIGSP M
Sbjct: 181 QSMEDTTMIYVTHDQVEAMTLADRICVLRDGRVEQIGTPLELYEKPNSLFVAGFIGSPKM 240

Query: 240 NFFRG-EVEPKDGRSFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEAR---D 295
           NF  G   EP                  + AHT         +GLR EH+ +   R    
Sbjct: 241 NFLTGPHAEP------------------FGAHT---------VGLRSEHLAIVPERGHWS 273

Query: 296 GEPTHQAVVDIEEPMGADNLLWLTFA-GQSMSVRIAGQRRYPPGSTVRLS 344
           G+  H       E +G+D  +++     + + VR +G     PG  + +S
Sbjct: 274 GQVVH------TEILGSDTYVYIDLGLEEPLVVRESGVSARKPGEALSIS 317


Lambda     K      H
   0.320    0.137    0.392 

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: 344
Number of extensions: 16
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: 361
Length of database: 333
Length adjustment: 29
Effective length of query: 332
Effective length of database: 304
Effective search space:   100928
Effective search space used:   100928
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