Align ABC transporter related (characterized, see rationale)
to candidate BWI76_RS10370 BWI76_RS10370 ABC transporter-like protein
Query= uniprot:B2TBJ9 (263 letters) >FitnessBrowser__Koxy:BWI76_RS10370 Length = 259 Score = 246 bits (628), Expect = 3e-70 Identities = 130/255 (50%), Positives = 175/255 (68%), Gaps = 4/255 (1%) Query: 7 VALSVKNIHKSFGDHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDDGSVS 66 V + ++ +HK FG VL+GI LD + G+ I+I+G SGSGKST LRCLN +E P G+V Sbjct: 6 VVMRIRALHKRFGAQSVLQGIDLDIYAGEKIAIIGGSGSGKSTLLRCLNFMEIPSAGTVE 65 Query: 67 LAGEEL-KMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPMRVQK 125 L G L K+ RG + +Q+ VR ++GMVFQ FNL+ H+TVL+N+ E + V+K Sbjct: 66 LDGVTLGKIDSRGQRRYS---EKQLSDVRQRVGMVFQQFNLFPHLTVLQNVSEALISVKK 122 Query: 126 RSRAESVEEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPTSAL 185 R E++ A A L KVGL K +P LSGGQQQRVAIARALAM P+++LFDEPTS+L Sbjct: 123 MRREEAMRIARAQLEKVGLGHKHQAWPGSLSGGQQQRVAIARALAMTPEIILFDEPTSSL 182 Query: 186 DPELVGEVLRVMRSLAEEGRTMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEVFVEC 245 DPELVGEVL +R LA+EGRT+L+VTHE+GFA H ++RV+F+ G + GT +EV Sbjct: 183 DPELVGEVLHTIRELADEGRTLLLVTHELGFAWHFADRVIFIENGVIHEMGTAEEVLRHP 242 Query: 246 KSDRFRQFVSSHQDR 260 + R + F+S +R Sbjct: 243 RQPRTQAFLSRFAER 257 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: 185 Number of extensions: 7 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: 259 Length adjustment: 25 Effective length of query: 238 Effective length of database: 234 Effective search space: 55692 Effective search space used: 55692 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