Align ABC transporter related (characterized, see rationale)
to candidate 8500099 DvMF_0862 ABC transporter related (RefSeq)
Query= uniprot:B2TBJ9 (263 letters) >FitnessBrowser__Miya:8500099 Length = 248 Score = 236 bits (602), Expect = 3e-67 Identities = 123/247 (49%), Positives = 169/247 (68%), Gaps = 11/247 (4%) Query: 9 LSVKNIHKSFGDHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDDGSVSLA 68 + + + K FG+ L +SLD G+ + I G SGSGKST LR +N LET D G++ + Sbjct: 10 IRISHAWKFFGELTALNDVSLDVMPGEKVVICGPSGSGKSTLLRSINRLETVDKGTIIVD 69 Query: 69 GEELKMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPMRVQKRSR 128 G+++ S ++++R +LGMVFQ+FNL+ H TVL+NL PMR++K R Sbjct: 70 GQDVN-----------SPDNDINKIRQELGMVFQSFNLFPHKTVLQNLTMAPMRLRKTPR 118 Query: 129 AESVEEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPTSALDPE 188 AE+ A LL KVG+++K +PA LSGGQQQRVAIARALAM+PK+MLFDEPTSALDPE Sbjct: 119 AEAESRALELLKKVGISDKANVFPAMLSGGQQQRVAIARALAMNPKIMLFDEPTSALDPE 178 Query: 189 LVGEVLRVMRSLAEEGRTMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEVFVECKSD 248 ++GEVL VM +LA EG TM+ VTHEMGFAR V++R++F+ GQV + P + F K Sbjct: 179 MIGEVLDVMVTLAREGMTMVCVTHEMGFAREVADRIIFMDHGQVLEENAPQDFFGAPKHP 238 Query: 249 RFRQFVS 255 R ++F++ Sbjct: 239 RLQKFLN 245 Lambda K H 0.318 0.133 0.377 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: 161 Number of extensions: 3 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: 263 Length of database: 248 Length adjustment: 24 Effective length of query: 239 Effective length of database: 224 Effective search space: 53536 Effective search space used: 53536 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: 47 (22.7 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