Align ABC transporter related (characterized, see rationale)
to candidate Ac3H11_4899 ABC transporter ATP-binding protein
Query= uniprot:B2TBJ9 (263 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4899 Length = 264 Score = 233 bits (595), Expect = 2e-66 Identities = 127/254 (50%), Positives = 174/254 (68%), Gaps = 10/254 (3%) Query: 6 PVALSVKNIHKSFGDHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDDGSV 65 P + + + KS+G + VLKGI L +G+VI+I+G SGSGKST LRC+N LE +G++ Sbjct: 21 PPIVDITALRKSYGSNEVLKGIDLKVQRGEVIAIIGKSGSGKSTLLRCVNGLEEFQEGAL 80 Query: 66 SLAGEELKMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPMRVQK 125 S+ G++L P+ R++ R Q+GM+FQ+FNL+ H++V N++ P V+ Sbjct: 81 SVNGKKLLHD-------SPTAMREL---RQQVGMIFQSFNLFPHLSVGRNIMLAPTLVKA 130 Query: 126 RSRAESVEEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPTSAL 185 R + +A LL +VGLAEK P LSGGQQQRVAIARALAM P+V+L DE TSAL Sbjct: 131 RDAKTAETQARKLLERVGLAEKFDAMPDQLSGGQQQRVAIARALAMEPQVLLCDEITSAL 190 Query: 186 DPELVGEVLRVMRSLAEEGRTMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEVFVEC 245 DPELVGEVLRV+ SLA+EG T+++VTHEM FAR V +RV+F+HQG+V GTP +F Sbjct: 191 DPELVGEVLRVVESLAQEGMTLMMVTHEMAFARKVGDRVIFMHQGRVHEQGTPAALFGNP 250 Query: 246 KSDRFRQFVSSHQD 259 ++ +QF+SS D Sbjct: 251 QTPELQQFLSSLHD 264 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: 208 Number of extensions: 5 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: 264 Length adjustment: 25 Effective length of query: 238 Effective length of database: 239 Effective search space: 56882 Effective search space used: 56882 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: 47 (22.7 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