Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate Dsui_0258 Dsui_0258 sulfate ABC transporter, ATP-binding protein
Query= BRENDA::Q97UY8 (353 letters) >FitnessBrowser__PS:Dsui_0258 Length = 360 Score = 193 bits (491), Expect = 5e-54 Identities = 117/351 (33%), Positives = 191/351 (54%), Gaps = 37/351 (10%) Query: 4 IIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELY 63 I ++N++K F G VALD+V+++I GE +LGPSG GKTT +RIIAG++ G++ Sbjct: 3 IEIRNIAKRF--GNFVALDDVSLSIPTGELVALLGPSGCGKTTLLRIIAGMETADEGQVM 60 Query: 64 FDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKE-----EIR 118 F+ + +R++G VFQ +AL+ ++ FEN+AF L +K KE EIR Sbjct: 61 FEGSEATH-----LHARERQVGFVFQHYALFRHMNVFENVAFGL-RVKPRKERPCESEIR 114 Query: 119 KRVEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDS 178 KRV ++ ++ + + + +P +LSGGQ+QR+ALARAL +P +LLLDEPF LD ++R Sbjct: 115 KRVMDLLSLVQLDWLADRYPTQLSGGQRQRIALARALAVEPKVLLLDEPFGALDTKVRKE 174 Query: 179 ARALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVA 238 R ++ + + ++ + V+HD + +ADRV V+ KG++ QVG P+++Y NP S V Sbjct: 175 LRRWLRRLHDEMHISSVFVTHDQEEALEVADRVVVMNKGRIEQVGSPDEVYSNPASPFVY 234 Query: 239 SLIGEINELEGKVTNEGVVIGSLRFPVSVSSDRAIIGIRPEDVKLSKDVIKDDSWILVGK 298 +G +N +V + P + A+ IRP D+ + + + Sbjct: 235 QFLGNVNVFHSRVHGAWAEVARDDVP---AGQEAVAFIRPHDIDIDTVATPESL-----E 286 Query: 299 GKVKVIGYQGGLFRITITPLDSEEEIFTYSDHPIHSGEEVLVYVRKDKIKV 349 KV + G L R+ + IH GE V V + +++ +V Sbjct: 287 AKVSYVQTIGPLVRVEV----------------IHQGELVEVELTRERQQV 321 Lambda K H 0.319 0.139 0.390 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: 322 Number of extensions: 13 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: 353 Length of database: 360 Length adjustment: 29 Effective length of query: 324 Effective length of database: 331 Effective search space: 107244 Effective search space used: 107244 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 (21.7 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