GapMind for catabolism of small carbon sources

 

Alignments for a candidate for msiK in Desulfovibrio vulgaris Miyazaki F

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 8500851 DvMF_1589 ABC transporter related (RefSeq)

Query= TCDB::P96483
         (377 letters)



>FitnessBrowser__Miya:8500851
          Length = 354

 Score =  218 bits (554), Expect = 3e-61
 Identities = 132/335 (39%), Positives = 190/335 (56%), Gaps = 35/335 (10%)

Query: 20  AVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVT------HLP 73
           AVD L++ I  GE   ++GPSGCGK+T+LRM+AG ED++ G I +GDR ++      +LP
Sbjct: 18  AVDSLNLEIGRGECFSMLGPSGCGKTTTLRMVAGFEDLDDGEIHVGDRLLSARRNNYYLP 77

Query: 74  PKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKP 133
           P+ RD  MVFQ +A++PH++V +N+ F L+I  +  AEI ++  EA     L     + P
Sbjct: 78  PEKRDFGMVFQAFAVWPHLSVYENVAFPLRIRRLSAAEIDRRTREALHHTSLADVAQKSP 137

Query: 134 KALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVT 193
             LSGG +QRVA+ RA+   P V L+DEPLS+LD  LR   R +I  LQR  G + +YVT
Sbjct: 138 DDLSGGGKQRVALARALAINPDVMLLDEPLSSLDPHLREEMRFEIKDLQRTFGFSILYVT 197

Query: 194 HDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPAMNLVEVPITDGGV 253
           HDQ EAM + DR+ V+++G++QQV +P ++Y  PAN FV GFIG    N ++V +T    
Sbjct: 198 HDQSEAMALSDRIMVMRNGVVQQVGTPLDVYTNPANSFVFGFIG--LSNFLDVNLTP--- 252

Query: 254 KFGNSVVPVNREALSAADKGDRTVTVGVRPEHFDVVELGGAVAASLSKDSADAPAGLAVS 313
                      E L   + GD  VT    P    +V  G A  AS   +           
Sbjct: 253 -----------EGLVRVNGGDARVTPAT-PPSARLVSAGRAALASRPSE----------- 289

Query: 314 VNVVEELGADGYVYGTAEVGGEVKDLVVRVNGRQV 348
           ++   E G  G V   A + GE+ D  + V+G++V
Sbjct: 290 IDFTAEGGLRGVVRRRAYL-GEIVDYRIDVSGQEV 323


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: 340
Number of extensions: 12
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: 354
Length adjustment: 30
Effective length of query: 347
Effective length of database: 324
Effective search space:   112428
Effective search space used:   112428
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