GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc04256 in Desulfovibrio vulgaris Hildenborough

Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate 208681 DVU3161 ABC transporter, ATP-binding protein

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



>MicrobesOnline__882:208681
          Length = 349

 Score =  269 bits (687), Expect = 9e-77
 Identities = 161/360 (44%), Positives = 225/360 (62%), Gaps = 15/360 (4%)

Query: 1   MTSVSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQI 60
           M+++ +  +S ++G V  +D ++ +++ G+ LVLLG SGCGKST L  IAGL  V+ G+I
Sbjct: 1   MSTIVLDKVSRHWGDVRAVDDVSFEVEQGDMLVLLGPSGCGKSTTLRLIAGLESVTSGRI 60

Query: 61  FIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEI 120
            I  R+VT   P  R + MVFQSYAL+P +TV  N+ FGL V K+P AE +KR+ RA EI
Sbjct: 61  LIGGRDVTNLPPAQRQLAMVFQSYALFPHLTVRDNILFGLVVRKVPAAERQKRLDRAVEI 120

Query: 121 LQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLH 180
           L +  LL+RKP ELSGGQ+QRVA+GRALV +  V L DEPLSNLDAKLR E+R EI+ L 
Sbjct: 121 LGLGKLLERKPGELSGGQQQRVALGRALVAEAAVCLMDEPLSNLDAKLRQEMRREIRALQ 180

Query: 181 QSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMN 240
           Q+L  TM+YVTHDQ EA+++ADRI +M+ G I Q A P  +Y+ P   F   FIG+P MN
Sbjct: 181 QTLGMTMVYVTHDQTEAMSMADRIILMQGGRIVQNATPTEMYSRPATAFAGSFIGTPPMN 240

Query: 241 FFRGEVEPKDGRSFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEARDGEPTH 300
             R  ++  D    V AG  +  VT +        G   +LG+RPEH+++ +  DG    
Sbjct: 241 LVR--LQGNDDGIRV-AGSRSGRVTCH-------AGADCMLGIRPEHIRIVD--DG---W 285

Query: 301 QAVVDIEEPMGADNLLWLTFAGQSMSVRIAGQRRYPPGSTVRLSFDMGVASIFDAESENR 360
           +AVV+  E +G++++L      + +SV + G      G+ + L        IFDA +  R
Sbjct: 286 RAVVESVEYLGSNSVLSCRVGSEELSVVVHGVTDTVVGAEIYLHCPEEHVHIFDAATGAR 345


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: 316
Number of extensions: 11
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: 349
Length adjustment: 29
Effective length of query: 332
Effective length of database: 320
Effective search space:   106240
Effective search space used:   106240
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 17 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