Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate N515DRAFT_4212 N515DRAFT_4212 multiple sugar transport system ATP-binding protein
Query= TCDB::Q9KKE1 (275 letters) >FitnessBrowser__Dyella79:N515DRAFT_4212 Length = 364 Score = 140 bits (352), Expect = 5e-38 Identities = 84/225 (37%), Positives = 130/225 (57%), Gaps = 8/225 (3%) Query: 41 VGLNDVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFDGDNIL-DLGAKAL 99 VG+ + S +I G++ V++G SG GK+TL+R I L E SG L G+ ++ D+ K Sbjct: 18 VGVAEASFEIADGELLVLVGPSGCGKTTLLRMIAGL-ESISGGTLSIGERVVNDIAPKD- 75 Query: 100 RAFRMRRVSMVFQSFALMPHRTVLQNVVYGQRVRGVSKDDAREIGMKWIDTVGLSGYDAK 159 R ++MVFQ++AL PH TV +N+ +G ++RG K + + + L Sbjct: 76 -----RDIAMVFQNYALYPHMTVAENLGFGLKLRGQPKAEIERRVAEAARMLELEQRLDS 130 Query: 160 FPHQLSGGMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQLLQLQRNLAKTIVF 219 P LSGG +QRV L RAL D V L+DE S LD +R M+ ++ ++ + L T+V+ Sbjct: 131 RPAALSGGQRQRVALGRALVRDPKVFLLDEPLSNLDAKLRLSMRVEIARIHQRLKATMVY 190 Query: 220 ITHDLDEALRIGSEIAILRDGQVVQVGTPNDILDNPANDYVARFV 264 +THD EA+ +G I +L G + Q+ TP ++ D PAN +VA F+ Sbjct: 191 VTHDQIEAMTLGQRIVVLNGGVIQQIDTPMNLYDTPANLFVAGFL 235 Lambda K H 0.323 0.139 0.397 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: 244 Number of extensions: 16 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: 275 Length of database: 364 Length adjustment: 27 Effective length of query: 248 Effective length of database: 337 Effective search space: 83576 Effective search space used: 83576 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 (21.9 bits) S2: 48 (23.1 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