Align ABC transporter related (characterized, see rationale)
to candidate AO353_28150 AO353_28150 arginine aminotransferase
Query= uniprot:B2TBJ9 (263 letters) >FitnessBrowser__pseudo3_N2E3:AO353_28150 Length = 667 Score = 334 bits (857), Expect = 3e-96 Identities = 169/256 (66%), Positives = 202/256 (78%) Query: 5 APVALSVKNIHKSFGDHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDDGS 64 A + V +HK FG+ VLKG+SL A +GDVIS++GASGSGKST LRC+N+LE PD G Sbjct: 412 AKTMIEVDGLHKRFGNIEVLKGVSLTAREGDVISLIGASGSGKSTLLRCINMLEVPDQGR 471 Query: 65 VSLAGEELKMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPMRVQ 124 + + GE +++ G SD +Q+ R+RS LGMVFQNFNLW H TVLENLIE P +V Sbjct: 472 ILVDGESIQLNFDRPGAPLVSDAKQLVRIRSSLGMVFQNFNLWPHRTVLENLIEAPTQVL 531 Query: 125 KRSRAESVEEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPTSA 184 + SRAE+ E AEALL +VGLA KR YPA LSGGQQQRVAIARALAM PKVMLFDEPTSA Sbjct: 532 RESRAEATERAEALLERVGLAAKRNEYPAFLSGGQQQRVAIARALAMRPKVMLFDEPTSA 591 Query: 185 LDPELVGEVLRVMRSLAEEGRTMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEVFVE 244 LDPELVGEVLRV+RSLAEEGRTM++VTHEM FAR VS++V +LHQG +E G+PDEVFV Sbjct: 592 LDPELVGEVLRVIRSLAEEGRTMILVTHEMAFARDVSSKVAYLHQGLIEEAGSPDEVFVH 651 Query: 245 CKSDRFRQFVSSHQDR 260 +S+R RQFV++HQ R Sbjct: 652 PRSERCRQFVNAHQTR 667 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: 410 Number of extensions: 13 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: 263 Length of database: 667 Length adjustment: 31 Effective length of query: 232 Effective length of database: 636 Effective search space: 147552 Effective search space used: 147552 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: 50 (23.9 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