Align ABC transporter related (characterized, see rationale)
to candidate 7026313 Shewana3_3455 ABC transporter related (RefSeq)
Query= uniprot:B2TBJ9 (263 letters) >FitnessBrowser__ANA3:7026313 Length = 656 Score = 140 bits (352), Expect = 9e-38 Identities = 86/235 (36%), Positives = 137/235 (58%), Gaps = 23/235 (9%) Query: 9 LSVKNIHKSF--GDHH--VLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDDGS 64 L V ++SF G+ VLK I+L +G++++I+GASGSGKST + L L+ P GS Sbjct: 6 LEVSACYRSFQAGEQQLTVLKDINLSIARGEMVAIVGASGSGKSTLMNILGCLDKPSKGS 65 Query: 65 VSLAGEELKMKRRGDGKLQPSDRRQVDRV----RSQLGMVFQNFNLWSHMTVLENLIEGP 120 + G++ + + VD + R G +FQ ++L + + N +E P Sbjct: 66 YFIDGQD-------------TSQMDVDELAKLRREHFGFIFQRYHLLGDLNAVGN-VEVP 111 Query: 121 MRVQKRSRAESVEEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDE 180 + R E E AE+LL+++GL E+ H P LSGGQQQRV++ARAL V+L DE Sbjct: 112 AVYAGKDRLERRERAESLLSRLGLGERLDHKPNQLSGGQQQRVSVARALMNGGDVILADE 171 Query: 181 PTSALDPELVGEVLRVMRSLAEEGRTMLVVTHEMGFARHVSNRVMFLHQGQVEAD 235 PT ALD E++R+++ L EG+T+++VTH+M A+H ++R++ + G + +D Sbjct: 172 PTGALDSHSGEEMMRLLQELHREGQTIIIVTHDMHVAQH-ADRIIEIKDGVIISD 225 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: 343 Number of extensions: 11 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: 656 Length adjustment: 31 Effective length of query: 232 Effective length of database: 625 Effective search space: 145000 Effective search space used: 145000 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