Align ABC transporter related (characterized, see rationale)
to candidate GFF2657 PS417_13545 arginine aminotransferase
Query= uniprot:B2TBJ9 (263 letters) >FitnessBrowser__WCS417:GFF2657 Length = 664 Score = 343 bits (880), Expect = 5e-99 Identities = 173/258 (67%), Positives = 207/258 (80%) Query: 3 ATAPVALSVKNIHKSFGDHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDD 62 A A + V ++HK FG+ VLKGISL AH+GDVIS++GASGSGKST LRC+N+LE PD Sbjct: 407 AEAKKMIEVIDLHKRFGNIEVLKGISLTAHEGDVISLIGASGSGKSTLLRCINMLEVPDQ 466 Query: 63 GSVSLAGEELKMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPMR 122 GS+ + GE +K+ G +D RQ+ R+RS LGMVFQNFNLW H TVLENLIE P + Sbjct: 467 GSIHVDGESIKLNYGRPGAPLVADARQLVRIRSTLGMVFQNFNLWPHRTVLENLIEAPTQ 526 Query: 123 VQKRSRAESVEEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPT 182 V + SRAE++E AEALL +VGLA KR YPA LSGGQQQRVAIARALAM PKVMLFDEPT Sbjct: 527 VLRESRAEAIERAEALLERVGLAAKRNEYPAFLSGGQQQRVAIARALAMRPKVMLFDEPT 586 Query: 183 SALDPELVGEVLRVMRSLAEEGRTMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEVF 242 SALDPELVGEVLRV+RSLAEEGRTM++VTHEM FAR VS++V FLHQG +E G+PD VF Sbjct: 587 SALDPELVGEVLRVIRSLAEEGRTMILVTHEMAFARDVSSKVAFLHQGMIEETGSPDAVF 646 Query: 243 VECKSDRFRQFVSSHQDR 260 ++ +S+R RQFV++HQ R Sbjct: 647 IDPRSERCRQFVNAHQTR 664 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: 419 Number of extensions: 10 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: 664 Length adjustment: 31 Effective length of query: 232 Effective length of database: 633 Effective search space: 146856 Effective search space used: 146856 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