Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate N515DRAFT_4212 N515DRAFT_4212 multiple sugar transport system ATP-binding protein
Query= CharProtDB::CH_001555 (400 letters) >FitnessBrowser__Dyella79:N515DRAFT_4212 Length = 364 Score = 155 bits (393), Expect = 1e-42 Identities = 85/223 (38%), Positives = 132/223 (59%), Gaps = 6/223 (2%) Query: 42 LGVKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELR 101 +GV +AS I +GE+ V++G SG GK+T++R++ L + G + I + I+ + Sbjct: 18 VGVAEASFEIADGELLVLVGPSGCGKTTLLRMIAGLESISGGTLSIGERVVNDIAPKD-- 75 Query: 102 EVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAGINAEERREKALDALRQVGLENYAHSY 161 + IAMVFQ++AL PHMTV +N FG++L G E + +A R + LE S Sbjct: 76 ----RDIAMVFQNYALYPHMTVAENLGFGLKLRGQPKAEIERRVAEAARMLELEQRLDSR 131 Query: 162 PDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFI 221 P LSGG RQRV L RAL +P + L+DE S LD +R M+ E+ ++ + + T+V++ Sbjct: 132 PAALSGGQRQRVALGRALVRDPKVFLLDEPLSNLDAKLRLSMRVEIARIHQRLKATMVYV 191 Query: 222 SHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTF 264 +HD EAM +G RI ++ G + Q+ TP + + PAN +V F Sbjct: 192 THDQIEAMTLGQRIVVLNGGVIQQIDTPMNLYDTPANLFVAGF 234 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: 326 Number of extensions: 12 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: 364 Length adjustment: 30 Effective length of query: 370 Effective length of database: 334 Effective search space: 123580 Effective search space used: 123580 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: 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