GapMind for catabolism of small carbon sources

 

Alignments for a candidate for msiK in Herbaspirillum seropedicae SmR1

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 HSERO_RS02210 HSERO_RS02210 sugar ABC transporter ATP-binding protein

Query= TCDB::P96483
         (377 letters)



>FitnessBrowser__HerbieS:HSERO_RS02210
          Length = 372

 Score =  303 bits (776), Expect = 5e-87
 Identities = 175/379 (46%), Positives = 224/379 (59%), Gaps = 39/379 (10%)

Query: 1   MATVTFDKATRIYPGSDKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGG 60
           MA V+     + Y   D   +  +++ IEDGEF+V VGPSGCGKST LRM+AGLE+++ G
Sbjct: 1   MAAVSIRNLAKRY--DDNEVMRDINLEIEDGEFVVFVGPSGCGKSTLLRMIAGLEEISDG 58

Query: 61  AIRIGDRDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAA 120
            + IG R +  +P   R +AMVFQ+YALYPHM++ DNM F LKIAG  KAEI   V+ AA
Sbjct: 59  DLDIGARRMNEVPASKRGVAMVFQSYALYPHMSLYDNMAFGLKIAGKSKAEIDAAVQHAA 118

Query: 121 KILDLTQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAS 180
           KIL +   LDRKP+ALSGGQRQRVA+GRAI R+P VFL DEPLSNLDA LRV  R + A 
Sbjct: 119 KILHIDHLLDRKPRALSGGQRQRVAIGRAITRQPSVFLFDEPLSNLDAALRVKMRLEFAK 178

Query: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPA 240
           L   L  T +YVTHDQ+EAMT+ D++ VL +G ++QV SP+ +Y  PAN FVAGFIGSP 
Sbjct: 179 LHDDLKTTMIYVTHDQIEAMTLADKIVVLSEGRIEQVGSPQQLYHHPANRFVAGFIGSPK 238

Query: 241 MNL------------VEVPITDGGVKFGNSVVPVNREALSAADKGDRTVTVGVRPEHFDV 288
           MN             V+V +  GG+++      V+   L    K    VT+GVRPEH ++
Sbjct: 239 MNFIDGTVAAIQADGVQVQLPGGGLQW----AAVDGSTLQVGQK----VTLGVRPEHLNI 290

Query: 289 VELGGAVAASLSKDSADAPAGLAVSVNVVEELGADGYVYGTAEVGGEVKDLVVRVNGRQV 348
                          A   A L      +E LG   Y+Y   E  G    L++RV     
Sbjct: 291 ---------------AQGQAALQARCTALELLGDFSYLYAAYE--GSEDALILRVPDSLD 333

Query: 349 PEKGSTLHVVPRPGETHVF 367
              GS L +   P   H+F
Sbjct: 334 APHGSVLPLAADPARCHLF 352


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: 389
Number of extensions: 14
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: 372
Length adjustment: 30
Effective length of query: 347
Effective length of database: 342
Effective search space:   118674
Effective search space used:   118674
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