Align ABC transporter related (characterized, see rationale)
to candidate Echvi_4044 Echvi_4044 ABC-type transport system involved in resistance to organic solvents, ATPase component
Query= uniprot:B2TBJ9 (263 letters) >FitnessBrowser__Cola:Echvi_4044 Length = 249 Score = 146 bits (368), Expect = 5e-40 Identities = 86/248 (34%), Positives = 143/248 (57%), Gaps = 14/248 (5%) Query: 9 LSVKNIHKSFGDHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDDGSVSLA 68 + V+ + KSFG+ VL G+ LD ++G+ + +LG SG+GKS ++ + L T D+G++++ Sbjct: 6 VEVRGLKKSFGELDVLMGVDLDLYKGENVVVLGKSGTGKSVLIKIMVGLLTQDEGTMNVL 65 Query: 69 GEELKMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPM--RVQKR 126 G+E+ D ++ +R ++G FQ L+ MTV ENL E P+ V+ Sbjct: 66 GKEVSNLGAKD----------LNELRLKIGFSFQASALYDSMTVRENL-EFPLVRNVKGL 114 Query: 127 SRAESVEEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPTSALD 186 SR E + E +L VGL++ P+ LSGGQ++R+ IAR L + P++ML+DEPT+ LD Sbjct: 115 SRTEKDKMVEEVLEAVGLSQTINQMPSELSGGQRKRIGIARTLILKPEIMLYDEPTAGLD 174 Query: 187 PELVGEVLRVMRSLAEEGRT-MLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEVFVEC 245 P ++ ++ + E T +++TH++ AR +RV L GQ A+G +EVF Sbjct: 175 PITCSDINNLINEVRENYNTSSIIITHDLTCARDTGDRVAVLLDGQFGAEGKFEEVFKTP 234 Query: 246 KSDRFRQF 253 + R + F Sbjct: 235 EDQRVKSF 242 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: 123 Number of extensions: 5 Number of successful extensions: 4 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: 249 Length adjustment: 24 Effective length of query: 239 Effective length of database: 225 Effective search space: 53775 Effective search space used: 53775 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