Align TreV, component of Trehalose porter (characterized)
to candidate 8502259 DvMF_2969 ABC transporter related (RefSeq)
Query= TCDB::Q97ZC0 (324 letters) >FitnessBrowser__Miya:8502259 Length = 418 Score = 210 bits (535), Expect = 4e-59 Identities = 106/228 (46%), Positives = 152/228 (66%) Query: 8 IVKKYGKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIADGADIT 67 +VK++ K +N ++ ++E G FF ILGPSG GK+TLL+++AG E D G I G D+ Sbjct: 34 LVKRFEKFTAVNDVSFEVEQGRFFSILGPSGCGKTTLLRMIAGFESPDSGVIAIRGRDMA 93 Query: 68 DKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLGISEILD 127 P +R V ++FQ+ AL+P MSV +N+AF LK RGM EI RV+ + +G+ Sbjct: 94 GIAPNRRPVNLIFQHLALFPMMSVAENVAFGLKRRGMAGGEISRRVQDVLERVGLPGYGV 153 Query: 128 KKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKELKGTFI 187 K Q+SGGQ+QRVA+AR +V P+ LLDEPL LD ++R + ELK +Q E+ TF+ Sbjct: 154 KMPAQLSGGQKQRVAIARCLVLEPAVLLLDEPLGALDLKLREQMKVELKTLQAEVGTTFV 213 Query: 188 YVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGE 235 Y+THDQ EAL ++D +A+++ G+FEQV P+ LY P + +VA FVGE Sbjct: 214 YITHDQSEALVMSDHVAVMNAGRFEQVDTPRNLYRRPASAFVAGFVGE 261 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: 284 Number of extensions: 8 Number of successful extensions: 1 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: 418 Length adjustment: 30 Effective length of query: 294 Effective length of database: 388 Effective search space: 114072 Effective search space used: 114072 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