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 BPHYT_RS35680 BPHYT_RS35680 sugar ABC transporter ATP-binding protein
Query= TCDB::P96483 (377 letters) >FitnessBrowser__BFirm:BPHYT_RS35680 Length = 360 Score = 302 bits (774), Expect = 8e-87 Identities = 170/365 (46%), Positives = 230/365 (63%), Gaps = 26/365 (7%) Query: 17 DKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTHLPPKD 76 D V +D+ I+DGEF+VLVGPSGCGKST +RM+AGLE+++GG + IG L P+ Sbjct: 15 DTQVVHGIDLDIDDGEFVVLVGPSGCGKSTLMRMVAGLEEISGGDLMIGGTRANSLAPQQ 74 Query: 77 RDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPKAL 136 R+I+MVFQ+YALYPH++V +N+ F +I A + ++E AAK+L+L YLDR P+AL Sbjct: 75 RNISMVFQSYALYPHLSVYENIAFGPRIRKESSASFKPRIEAAAKMLNLGGYLDRLPRAL 134 Query: 137 SGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHDQ 196 SGGQRQRVAMGRA+VREP +FL DEPLSNLDAKLRV RT+I +L +RL T +YVTHDQ Sbjct: 135 SGGQRQRVAMGRAVVREPSLFLFDEPLSNLDAKLRVQMRTEIKALHQRLKNTVIYVTHDQ 194 Query: 197 VEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPAMNLVEVPITDGGVKFG 256 +EAMTM DR+ V+ G ++Q+ P +YD PANLFVA F+GSP+MN E I G Sbjct: 195 IEAMTMADRIVVMNAGRIEQIGRPLELYDHPANLFVASFLGSPSMNFAEGVIASRAQGQG 254 Query: 257 NSV-----VPVNREALSAADKGDRTVTVGVRPEHFDVVELGGAVAASLSKDSADAPAGLA 311 ++ + E A+ VT+GVRPEH + + + DA Sbjct: 255 LALNLTGGGEIVLEGAPASAVVGAKVTLGVRPEHIETM-----------TPTPDA----T 299 Query: 312 VSVNVVEELGADGYVYGTAEVGGEVKDLVVRVNGRQVPEKGSTLHVVPRPGE-THVFSTS 370 + V VVE GA+ ++YG ++GG + R + P + TL + P E H+F T Sbjct: 300 MEVEVVEPTGAETHLYG--KIGGSTWCVTTRQRSKIEPGQRVTLRL---PAEHIHLFDTE 354 Query: 371 TGERL 375 +G RL Sbjct: 355 SGRRL 359 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: 392 Number of extensions: 21 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: 360 Length adjustment: 30 Effective length of query: 347 Effective length of database: 330 Effective search space: 114510 Effective search space used: 114510 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