GapMind for catabolism of small carbon sources

 

Alignments for a candidate for msiK in Phaeobacter inhibens BS107

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 GFF262 PGA1_c02740 sn-glycerol-3-phosphate import ATP-binding protein UgbC

Query= TCDB::P96483
         (377 letters)



>FitnessBrowser__Phaeo:GFF262
          Length = 348

 Score =  339 bits (870), Expect = 6e-98
 Identities = 187/374 (50%), Positives = 246/374 (65%), Gaps = 27/374 (7%)

Query: 1   MATVTFDKATRIYPGSDKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGG 60
           MA VT +   ++YP   + AV      IEDGEF+VLVGPSGCGKST LRM+AGLED+  G
Sbjct: 1   MAQVTLNSVRKVYPNGVE-AVTSSSFKIEDGEFVVLVGPSGCGKSTLLRMIAGLEDITEG 59

Query: 61  AIRIGDRDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAA 120
            + IGDR V ++ P DRDIAMVFQNYALYPHMTV  N+ + LK    P+AEI+QKV EAA
Sbjct: 60  TLEIGDRVVNNVDPADRDIAMVFQNYALYPHMTVRKNIAYGLKNRKTPEAEIKQKVAEAA 119

Query: 121 KILDLTQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAS 180
           K+L+L +YLDRKP  LSGGQRQRVAMGRAIVR+P +FL DEPLSNLDAKLR   R +I +
Sbjct: 120 KMLNLEEYLDRKPSQLSGGQRQRVAMGRAIVRDPALFLFDEPLSNLDAKLRNQMRIEIKA 179

Query: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPA 240
           LQRRLG+T++YVTHDQVEAMTM DR+ VL  G ++Q+ +P  +Y  PA++FVA F+G+P 
Sbjct: 180 LQRRLGVTSIYVTHDQVEAMTMADRIIVLNGGRIEQIGTPSEIYHNPASVFVASFMGAPP 239

Query: 241 MNLVEVPITDGGVKFGNSVVPVNREALSAADKGDRTVTVGVRPEHFDVVELGGAVAASLS 300
           MNL++  I +G V   +    V+  AL  + +G   V +G+RPE   +V           
Sbjct: 240 MNLLDATIANGQVTLPDG---VSMGALDTSAQG--AVKLGIRPEDVQLV----------- 283

Query: 301 KDSADAPAGLAVSVNVVEELGADGYVYGTAEVGGEVKDLVVRVNGRQVPEKGSTLHVVPR 360
                A  GLA+ V ++EELGA   ++G  ++GG+   + V    + +P    T  +   
Sbjct: 284 -----AEGGLAIDVELIEELGAHRLLHG--KLGGQPFTIHVL---KDIPVDPGTHQISVD 333

Query: 361 PGETHVFSTSTGER 374
           P    +F   +G+R
Sbjct: 334 PAAICLFDAESGQR 347


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: 412
Number of extensions: 15
Number of successful extensions: 3
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: 348
Length adjustment: 29
Effective length of query: 348
Effective length of database: 319
Effective search space:   111012
Effective search space used:   111012
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