Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate 3607949 Dshi_1357 ABC transporter related (RefSeq)
Query= SwissProt::P17328 (400 letters) >FitnessBrowser__Dino:3607949 Length = 349 Score = 171 bits (433), Expect = 3e-47 Identities = 91/221 (41%), Positives = 131/221 (59%), Gaps = 6/221 (2%) Query: 44 VKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREV 103 +K L I +GE V +G SG GKST++R++ L + +RG +LIDGVD+ A Sbjct: 19 IKGVDLEIRDGEFVVFVGPSGCGKSTLLRMIGGLEDTSRGAMLIDGVDVTDHPPA----- 73 Query: 104 RRKKIAMVFQSFALMPHMTVLDNTAFGMELAGIAAQERREKALDALRQVGLENYAHAYPD 163 ++ + MVFQS+AL PHM+V +N F ++ AG A E EK A + LE Y P Sbjct: 74 -KRGLTMVFQSYALYPHMSVRENMGFSLKTAGAPAAEIAEKVEAAAAVLKLEPYLDRRPK 132 Query: 164 ELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISH 223 +LSGG RQRV + R++ P L DE S LD +R EM+ E+ KL T+++++H Sbjct: 133 DLSGGQRQRVAIGRSIVRAPTAFLFDEPLSNLDAALRVEMRYEIAKLHQSLDTTMIYVTH 192 Query: 224 DLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTF 264 D EAM + DRI +++ G++ QVGTP E+ PAN +V F Sbjct: 193 DQVEAMTLADRIVVLEFGKIAQVGTPRELYETPANLFVAQF 233 Lambda K H 0.319 0.137 0.378 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: 314 Number of extensions: 17 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: 400 Length of database: 349 Length adjustment: 30 Effective length of query: 370 Effective length of database: 319 Effective search space: 118030 Effective search space used: 118030 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: 50 (23.9 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