GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21106 in Desulfovibrio vulgaris Hildenborough

Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate 208681 DVU3161 ABC transporter, ATP-binding protein

Query= reanno::Smeli:SM_b21106
         (365 letters)



>MicrobesOnline__882:208681
          Length = 349

 Score =  263 bits (672), Expect = 5e-75
 Identities = 149/360 (41%), Positives = 209/360 (58%), Gaps = 17/360 (4%)

Query: 1   MAPVTLKKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAI 60
           M+ + L K+ + +G +  V  +  EV+  + + L+GPSGCGKSTTLR+IAGLE V+ G I
Sbjct: 1   MSTIVLDKVSRHWGDVRAVDDVSFEVEQGDMLVLLGPSGCGKSTTLRLIAGLESVTSGRI 60

Query: 61  EIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAI 120
            IGGR V +LPP  R ++MVFQSYAL+PH+TV +N+ F L +   PA E + R+  A  I
Sbjct: 61  LIGGRDVTNLPPAQRQLAMVFQSYALFPHLTVRDNILFGLVVRKVPAAERQKRLDRAVEI 120

Query: 121 LDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLH 180
           L L  LLER+P +LSGGQ+QRVA+GRA+V +  V L DEPLSNLDAKLR ++R EI+ L 
Sbjct: 121 LGLGKLLERKPGELSGGQQQRVALGRALVAEAAVCLMDEPLSNLDAKLRQEMRREIRALQ 180

Query: 181 ARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPMN 240
             +  TM+YVTHDQ EAM+++DRI++M+ G I Q  TP +++ RPAT F   FIG+PPMN
Sbjct: 181 QTLGMTMVYVTHDQTEAMSMADRIILMQGGRIVQNATPTEMYSRPATAFAGSFIGTPPMN 240

Query: 241 MEEAVLTDGKLAFASGATLPLPPRFRSLVREGQKVTFGLRPDDVYPSGHGLHAGDADAVH 300
           +      D  +  A   +       R     G     G+RP+ +     G  A   ++V 
Sbjct: 241 LVRLQGNDDGIRVAGSRS------GRVTCHAGADCMLGIRPEHIRIVDDGWRA-VVESVE 293

Query: 301 EIELPVTITEPLGNETLVFTQFNGRDWVSRMLNPRPLRPGEAVPMSFDLARAHLFDGETG 360
            +     ++  +G+E L        D V           G  + +       H+FD  TG
Sbjct: 294 YLGSNSVLSCRVGSEELSVVVHGVTDTV----------VGAEIYLHCPEEHVHIFDAATG 343


Lambda     K      H
   0.320    0.137    0.397 

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: 325
Number of extensions: 8
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: 365
Length of database: 349
Length adjustment: 29
Effective length of query: 336
Effective length of database: 320
Effective search space:   107520
Effective search space used:   107520
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