Align TreV, component of Trehalose porter (characterized)
to candidate 351279 BT1751 Glycine betaine transport ATP-binding protein (NCBI ptt file)
Query= TCDB::Q97ZC0 (324 letters) >FitnessBrowser__Btheta:351279 Length = 408 Score = 166 bits (419), Expect = 1e-45 Identities = 89/233 (38%), Positives = 141/233 (60%), Gaps = 6/233 (2%) Query: 7 DIVKKYGKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIADGADI 66 +I+K G + + I GE FVI+G SG GKSTLL+ + + + G++I +G DI Sbjct: 32 EILKATGCTVAVKDANLSINEGEIFVIMGLSGSGKSTLLRCINRLIRPTSGEVIINGTDI 91 Query: 67 ---TDKPP---EKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLL 120 +DK ++ +AMVFQN+ L P+ SV NIAF L+++G+KK E ++ ++ +L+ Sbjct: 92 AKVSDKELLQIRRKELAMVFQNFGLLPHRSVLHNIAFGLELQGVKKGEREQKAMESMQLV 151 Query: 121 GISEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQK 180 G+ ++ V+++SGG QQRV LARA+ NP L+DE S LD +R + EL +Q Sbjct: 152 GLKGYENQMVSELSGGMQQRVGLARALANNPEVLLMDEAFSALDPLIRVQMQDELLTLQS 211 Query: 181 ELKGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFV 233 ++K T +++THD EA+ L DRIAI+ G+ Q+ + + P +V +FV Sbjct: 212 KMKKTIVFITHDLSEAIKLGDRIAIMKDGEIVQIGTSEEILTEPANAYVERFV 264 Score = 23.9 bits (50), Expect = 0.007 Identities = 21/82 (25%), Positives = 37/82 (45%), Gaps = 12/82 (14%) Query: 1 MTVELIDIVKKYGKNIVI--NGITEKIETGEFFVILGPS-----GEGKSTLLK-----IL 48 M EL+ + K K IV + ++E I+ G+ I+ G + L + + Sbjct: 202 MQDELLTLQSKMKKTIVFITHDLSEAIKLGDRIAIMKDGEIVQIGTSEEILTEPANAYVE 261 Query: 49 AGIEKLDKGKIIADGADITDKP 70 +E +D+ KII + + DKP Sbjct: 262 RFVENVDRSKIITASSVMVDKP 283 Lambda K H 0.318 0.137 0.385 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: 318 Number of extensions: 15 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 324 Length of database: 408 Length adjustment: 29 Effective length of query: 295 Effective length of database: 379 Effective search space: 111805 Effective search space used: 111805 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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