Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate Dsui_0258 Dsui_0258 sulfate ABC transporter, ATP-binding protein
Query= TCDB::G3LHY9 (356 letters) >FitnessBrowser__PS:Dsui_0258 Length = 360 Score = 163 bits (413), Expect = 6e-45 Identities = 91/241 (37%), Positives = 143/241 (59%), Gaps = 7/241 (2%) Query: 24 SLKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQPSHGRILFDGKDVTNLSTQSRNI 83 +L +V G ALLGPSGCGKTTLL II+G+ G+++F+G + T+L + R + Sbjct: 17 ALDDVSLSIPTGELVALLGPSGCGKTTLLRIIAGMETADEGQVMFEGSEATHLHARERQV 76 Query: 84 AQVFQFPVIYDTMTVYDNLAFPLR----NRGVAEADVDRRVRDILEMIDLASWARRKAQG 139 VFQ ++ M V++N+AF LR E+++ +RV D+L ++ L A R Sbjct: 77 GFVFQHYALFRHMNVFENVAFGLRVKPRKERPCESEIRKRVMDLLSLVQLDWLADRYPTQ 136 Query: 140 LTADQKQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVLRSQLKRLHKQFGFTMVYVTH 199 L+ Q+Q+I+L R L + +L DEP +D ++ LR L+RLH + + V+VTH Sbjct: 137 LSGGQRQRIALARALAV-EPKVLLLDEPFGALDTKVRKELRRWLRRLHDEMHISSVFVTH 195 Query: 200 DQTEALTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGYFIGSPGMNFMPARIEGSTVK 259 DQ EAL A++VVVM G+I Q+G+P E++ P+ FV F+G+ +N +R+ G+ + Sbjct: 196 DQEEALEVADRVVVMNKGRIEQVGSPDEVYSNPASPFVYQFLGN--VNVFHSRVHGAWAE 253 Query: 260 V 260 V Sbjct: 254 V 254 Lambda K H 0.321 0.137 0.405 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: 279 Number of extensions: 9 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: 356 Length of database: 360 Length adjustment: 29 Effective length of query: 327 Effective length of database: 331 Effective search space: 108237 Effective search space used: 108237 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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