Align TreV, component of Trehalose porter (characterized)
to candidate WP_012048833.1 SWIT_RS13320 amino acid ABC transporter ATP-binding protein
Query= TCDB::Q97ZC0 (324 letters) >NCBI__GCF_000016765.1:WP_012048833.1 Length = 241 Score = 124 bits (311), Expect = 2e-33 Identities = 76/230 (33%), Positives = 124/230 (53%), Gaps = 12/230 (5%) Query: 3 VELIDIVKKYGKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIAD 62 + + + K YG + ++ + GE VI GPSG GKSTL++ + G+E D+G +I Sbjct: 2 IHMAGVGKWYGGYHALRNVSLDVARGERIVICGPSGSGKSTLIRCINGLETHDEG-VIRI 60 Query: 63 GADITDKPPEKR-------NVAMVFQNYALYPNMSVRDNIAF-PLKMRGMKKEEIIERVE 114 G D + P++R V MVFQ++ L+P++++ +N A P+K+RG+ ++ Sbjct: 61 GED--EVRPDRRVLQRIRARVGMVFQDFNLFPHLTILENCALAPMKVRGLARDAAEALAR 118 Query: 115 KAAKLLGISEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGE 174 + + + I++ DK Q+SGGQQQR A+ARA+ P L DEP S LDA + Sbjct: 119 ELLERVRIADQADKYPAQLSGGQQQRTAIARALAMQPEIILFDEPTSALDAEMVKEVLDI 178 Query: 175 LKRIQKELKGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYP 224 +K + E T + VTH+ A +ADRI + G+ + P+ + P Sbjct: 179 MKALATE-GITMLCVTHEMGFAREVADRIIFMDAGQIVETGSPRDFFTAP 227 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: 184 Number of extensions: 12 Number of successful extensions: 4 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: 324 Length of database: 241 Length adjustment: 26 Effective length of query: 298 Effective length of database: 215 Effective search space: 64070 Effective search space used: 64070 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: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. 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