Align ABC transporter related (characterized, see rationale)
to candidate 8500594 DvMF_1342 ABC transporter related (RefSeq)
Query= uniprot:B2TBJ9 (263 letters) >FitnessBrowser__Miya:8500594 Length = 243 Score = 253 bits (645), Expect = 3e-72 Identities = 134/250 (53%), Positives = 177/250 (70%), Gaps = 14/250 (5%) Query: 9 LSVKNIHKSF---GDHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDDGSV 65 ++ N+HK F H L+G+SL G+V+ I+G SGSGKSTFLRCLN LE D+G++ Sbjct: 2 INATNVHKFFYTPDKLHALRGVSLSVAPGEVVVIIGPSGSGKSTFLRCLNRLEYADEGAI 61 Query: 66 SLAGEELKMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPMRVQK 125 + G ++ L P +++ VR+++GMVFQ+FNL+ H+TVLENL V+K Sbjct: 62 RIEGRDI---------LDPDC--EINEVRAEVGMVFQSFNLFPHLTVLENLTLAQTTVRK 110 Query: 126 RSRAESVEEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPTSAL 185 R +AE+ ++ LL KVG+AEK YP LSGGQQQRVAIARALAM PK MLFDEPTSAL Sbjct: 111 RGKAEAEKKGMELLRKVGIAEKHNVYPDQLSGGQQQRVAIARALAMDPKAMLFDEPTSAL 170 Query: 186 DPELVGEVLRVMRSLAEEGRTMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEVFVEC 245 DPE+VGEVL VM++LA EG TM+VVTHEMGFAR V++RV+F+ QG + G+PD+ F Sbjct: 171 DPEMVGEVLDVMKNLAREGMTMVVVTHEMGFAREVADRVVFMDQGSILEVGSPDKFFTAP 230 Query: 246 KSDRFRQFVS 255 + DR + F+S Sbjct: 231 EHDRTKLFLS 240 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: 188 Number of extensions: 2 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: 243 Length adjustment: 24 Effective length of query: 239 Effective length of database: 219 Effective search space: 52341 Effective search space used: 52341 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: 46 (22.3 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