Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate 8500594 DvMF_1342 ABC transporter related (RefSeq)
Query= reanno::pseudo6_N2E2:Pf6N2E2_5405 (254 letters) >FitnessBrowser__Miya:8500594 Length = 243 Score = 274 bits (700), Expect = 1e-78 Identities = 143/243 (58%), Positives = 180/243 (74%), Gaps = 3/243 (1%) Query: 14 IIQMQGVNKWY---GQFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQGR 70 +I V+K++ + H L+ ++L+V GE +V+ GPSGSGKST +RCLNRLE +G Sbjct: 1 MINATNVHKFFYTPDKLHALRGVSLSVAPGEVVVIIGPSGSGKSTFLRCLNRLEYADEGA 60 Query: 71 IVVDGVELTNDLKQIEAIRREVGMVFQHFNLFPHLTILQNCTLAPMWVRKMPKRKAEEIA 130 I ++G ++ + +I +R EVGMVFQ FNLFPHLT+L+N TLA VRK K +AE+ Sbjct: 61 IRIEGRDILDPDCEINEVRAEVGMVFQSFNLFPHLTVLENLTLAQTTVRKRGKAEAEKKG 120 Query: 131 MHYLERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVKEVLD 190 M L +V I E+ + YP QLSGGQQQRVAIARAL M PK MLFDEPTSALDPEMV EVLD Sbjct: 121 MELLRKVGIAEKHNVYPDQLSGGQQQRVAIARALAMDPKAMLFDEPTSALDPEMVGEVLD 180 Query: 191 TMIGLAEDGMTMLCVTHEMGFARTVANRVIFMDKGEIVEQAAPNDFFDNPQNDRTKLFLS 250 M LA +GMTM+ VTHEMGFAR VA+RV+FMD+G I+E +P+ FF P++DRTKLFLS Sbjct: 181 VMKNLAREGMTMVVVTHEMGFAREVADRVVFMDQGSILEVGSPDKFFTAPEHDRTKLFLS 240 Query: 251 QIL 253 QIL Sbjct: 241 QIL 243 Lambda K H 0.322 0.137 0.407 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: 201 Number of extensions: 9 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: 254 Length of database: 243 Length adjustment: 24 Effective length of query: 230 Effective length of database: 219 Effective search space: 50370 Effective search space used: 50370 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 (21.9 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