GapMind for catabolism of small carbon sources

 

Alignments for a candidate for msiK in Paraburkholderia bryophila 376MFSha3.1

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 H281DRAFT_04155 H281DRAFT_04155 sorbitol ABC transporter ATP-binding protein /mannitol ABC transporter ATP-binding protein

Query= TCDB::P96483
         (377 letters)



>FitnessBrowser__Burk376:H281DRAFT_04155
          Length = 369

 Score =  306 bits (783), Expect = 8e-88
 Identities = 178/374 (47%), Positives = 225/374 (60%), Gaps = 25/374 (6%)

Query: 1   MATVTFDKATRIYPGSDKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGG 60
           MA+VT     + Y   D   +  +++ I DGEF+V VGPSGCGKST +RM+AGLED++GG
Sbjct: 1   MASVTLRNIRKAY--DDTEVMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGG 58

Query: 61  AIRIGDRDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAA 120
            + I    +  +PP  R IAMVFQ+YALYPHMT+ DNM F LK+AG  K EI   V  AA
Sbjct: 59  DLTINGTRMNDVPPAKRGIAMVFQSYALYPHMTLYDNMAFGLKLAGTKKPEIDAAVRNAA 118

Query: 121 KILDLTQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAS 180
           KIL +   LDRKPK LSGGQRQRVA+GRAI R+P+VFL DEPLSNLDA LRV  R + A 
Sbjct: 119 KILHIDHLLDRKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFAR 178

Query: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPA 240
           L   L  T +YVTHDQVEAMT+ D++ VL  G L+QV SP  +Y  PAN FVAGFIGSP 
Sbjct: 179 LHDELKTTMIYVTHDQVEAMTLADKIVVLSAGNLEQVGSPTMLYHAPANRFVAGFIGSPK 238

Query: 241 MNLVE---VPITDGGVKFGNSVVPVNREAL--SAADKGDRTVTVGVRPEHFDVVELGGAV 295
           MN +E     +T  GV          R A+   A  +GD+ VTVG+RPEH  V       
Sbjct: 239 MNFMEGVVQSVTHDGVTVRYETGETQRVAVEPGAVKQGDK-VTVGIRPEHLHV------- 290

Query: 296 AASLSKDSADAPAGLAVSVNVVEELGADGYVYGTAEVGGEVKDLVVRVNGRQVPEKGSTL 355
              ++ D      G++     VE LG   Y+Y  + V  +   L+ R+   +   KG T 
Sbjct: 291 --GMTDD------GVSARTMAVESLGDAAYLYAESSVAPD--GLIARIPPLERHAKGETQ 340

Query: 356 HVVPRPGETHVFST 369
            +   P   H+F +
Sbjct: 341 KLGATPEHCHLFDS 354


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: 415
Number of extensions: 17
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: 369
Length adjustment: 30
Effective length of query: 347
Effective length of database: 339
Effective search space:   117633
Effective search space used:   117633
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: 50 (23.9 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