Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate 3608008 Dshi_1416 ABC transporter related (RefSeq)
Query= BRENDA::Q97UY8 (353 letters) >FitnessBrowser__Dino:3608008 Length = 347 Score = 211 bits (537), Expect = 2e-59 Identities = 124/312 (39%), Positives = 189/312 (60%), Gaps = 22/312 (7%) Query: 1 MVRIIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTG 60 M I + +V K + G V +++ ++ I + E +LGPSG GKTT MR+IAGL+ PS+G Sbjct: 1 MAEIRLNHVQK--RWGSFVGVEDFHLTIPDREFLVLLGPSGCGKTTTMRMIAGLEEPSSG 58 Query: 61 ELYFDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKR 120 E++ DR+V + + P+DR + MVFQ++ LYPN+ +ENI FPL K+ + E R Sbjct: 59 EIWIGDRMVNA-----LDPKDRDVAMVFQSYGLYPNMNVYENIRFPLKVRKVPEVEHEAR 113 Query: 121 VEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSAR 180 V + ++++ L+ P LSGGQ+QRVALARA+V++P++ L+DEP SNLDA++R S R Sbjct: 114 VMRASAMVELDDFLHRKPAALSGGQRQRVALARAIVREPNVFLMDEPLSNLDAKLRVSTR 173 Query: 181 ALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASL 240 A +K + L VT + V+HD + +ADRV V+ G + QVG P ++YD P + VAS Sbjct: 174 AQIKNLSHELQVTTIYVTHDQIEAMTLADRVVVMSAGVVQQVGTPMEIYDRPANTFVASF 233 Query: 241 IGE--INELEGKVTN-----EGVVIGSLRFPVSVSSDRAIIGIRPEDVKLSKDVIKDDSW 293 IG +N +EG VT+ + V I L S ++ R +G R ED + V+ D Sbjct: 234 IGSPAMNLMEGAVTDGTFHGDRVAIAGL----SGAAGRVTLGFRAEDAQ----VVDSDGQ 285 Query: 294 ILVGKGKVKVIG 305 I ++++G Sbjct: 286 IAAPVYSMELLG 297 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: 266 Number of extensions: 15 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: 353 Length of database: 347 Length adjustment: 29 Effective length of query: 324 Effective length of database: 318 Effective search space: 103032 Effective search space used: 103032 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 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