GapMind for catabolism of small carbon sources

 

Alignments for a candidate for msiK in Desulfovibrio vulgaris Hildenborough

Align MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized)
to candidate 208681 DVU3161 ABC transporter, ATP-binding protein

Query= TCDB::P96483
         (377 letters)



>MicrobesOnline__882:208681
          Length = 349

 Score =  286 bits (732), Expect = 6e-82
 Identities = 165/374 (44%), Positives = 226/374 (60%), Gaps = 29/374 (7%)

Query: 1   MATVTFDKATRIYPGSDKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGG 60
           M+T+  DK +R +   D  AVD +   +E G+ LVL+GPSGCGKST+LR++AGLE V  G
Sbjct: 1   MSTIVLDKVSRHW--GDVRAVDDVSFEVEQGDMLVLLGPSGCGKSTTLRLIAGLESVTSG 58

Query: 61  AIRIGDRDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAA 120
            I IG RDVT+LPP  R +AMVFQ+YAL+PH+TV DN+ F L +  VP AE +++++ A 
Sbjct: 59  RILIGGRDVTNLPPAQRQLAMVFQSYALFPHLTVRDNILFGLVVRKVPAAERQKRLDRAV 118

Query: 121 KILDLTQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAS 180
           +IL L + L+RKP  LSGGQ+QRVA+GRA+V E  V LMDEPLSNLDAKLR   R +I +
Sbjct: 119 EILGLGKLLERKPGELSGGQQQRVALGRALVAEAAVCLMDEPLSNLDAKLRQEMRREIRA 178

Query: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPA 240
           LQ+ LG+T VYVTHDQ EAM+M DR+ +++ G + Q  +P  MY +PA  F   FIG+P 
Sbjct: 179 LQQTLGMTMVYVTHDQTEAMSMADRIILMQGGRIVQNATPTEMYSRPATAFAGSFIGTPP 238

Query: 241 MNLVEVPITDGGVKFGNSVVPVNREALSAADKGDRTVTVGVRPEHFDVVELGGAVAASLS 300
           MNLV +   D G++   S     R        G     +G+RPEH  +V+          
Sbjct: 239 MNLVRLQGNDDGIRVAGS-----RSGRVTCHAG-ADCMLGIRPEHIRIVD---------- 282

Query: 301 KDSADAPAGLAVSVNVVEELGADGYVYGTAEVGGEVKDLVVRVNGRQVPEKGSTLHVVPR 360
                   G    V  VE LG++  +  +  VG E  +L V V+G      G+ +++   
Sbjct: 283 -------DGWRAVVESVEYLGSNSVL--SCRVGSE--ELSVVVHGVTDTVVGAEIYLHCP 331

Query: 361 PGETHVFSTSTGER 374
               H+F  +TG R
Sbjct: 332 EEHVHIFDAATGAR 345


Lambda     K      H
   0.317    0.135    0.379 

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: 349
Number of extensions: 15
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: 377
Length of database: 349
Length adjustment: 29
Effective length of query: 348
Effective length of database: 320
Effective search space:   111360
Effective search space used:   111360
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 (21.6 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