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.
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:
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