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 Dsui_0258 Dsui_0258 sulfate ABC transporter, ATP-binding protein
Query= TCDB::P96483 (377 letters) >FitnessBrowser__PS:Dsui_0258 Length = 360 Score = 193 bits (491), Expect = 5e-54 Identities = 117/357 (32%), Positives = 188/357 (52%), Gaps = 32/357 (8%) Query: 20 AVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTHLPPKDRDI 79 A+D + ++I GE + L+GPSGCGK+T LR++AG+E + G + + THL ++R + Sbjct: 17 ALDDVSLSIPTGELVALLGPSGCGKTTLLRIIAGMETADEGQVMFEGSEATHLHARERQV 76 Query: 80 AMVFQNYALYPHMTVADNMGFALKIAGVPK----AEIRQKVEEAAKILDLTQYLDRKPKA 135 VFQ+YAL+ HM V +N+ F L++ + +EIR++V + ++ L DR P Sbjct: 77 GFVFQHYALFRHMNVFENVAFGLRVKPRKERPCESEIRKRVMDLLSLVQLDWLADRYPTQ 136 Query: 136 LSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHD 195 LSGGQRQR+A+ RA+ EP+V L+DEP LD K+R R + L + I++V+VTHD Sbjct: 137 LSGGQRQRIALARALAVEPKVLLLDEPFGALDTKVRKELRRWLRRLHDEMHISSVFVTHD 196 Query: 196 QVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPAMNLVEVPITDGGVKF 255 Q EA+ + DRV V+ G ++QV SP +Y PA+ FV F+G+ +N+ + + Sbjct: 197 QEEALEVADRVVVMNKGRIEQVGSPDEVYSNPASPFVYQFLGN--VNVFHSRVHGAWAEV 254 Query: 256 GNSVVPVNREALSAADKGDRTVTVGVRPEHFDVVELGGAVAASLSKDSADAPAGLAVSVN 315 VP +EA++ +RP D+ D+ P L V+ Sbjct: 255 ARDDVPAGQEAVAF-----------IRPHDIDI-------------DTVATPESLEAKVS 290 Query: 316 VVEELGADGYVYGTAEVGGEVKDLVVRVNGRQVPEKGSTLHVVPRPGETHVFSTSTG 372 V+ +G V GE+ ++ + +QV + V +P + VF+ G Sbjct: 291 YVQTIGP--LVRVEVIHQGELVEVELTRERQQVLGLTAGQQVWLKPRQVKVFANGEG 345 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: 328 Number of extensions: 20 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: 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 Apr 09 2024. 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