Align ATPase (characterized, see rationale)
to candidate Echvi_1582 Echvi_1582 ABC-type antimicrobial peptide transport system, ATPase component
Query= uniprot:Q31RN8 (261 letters) >FitnessBrowser__Cola:Echvi_1582 Length = 225 Score = 139 bits (349), Expect = 7e-38 Identities = 87/222 (39%), Positives = 139/222 (62%), Gaps = 14/222 (6%) Query: 25 EGVEKWYGNQFQALC---GVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEIWI 81 E V K Y + + L ++L+V+ G+ + ++GPSGSGK+T L L+S G + + Sbjct: 7 ENVSKIYQSGSRTLTVLEDINLSVKAGDSIAIVGPSGSGKTTLLGLCAGLDSASSGSVAL 66 Query: 82 EGHRL---SHDRRDIATIR-QEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAEAT 137 GHRL S D+R A +R QE+G +FQ F L P LT L+N+M+ P+++++ A+ +AT Sbjct: 67 NGHRLEGLSEDQR--AAVRSQEIGFIFQNFQLLPTLTALENVMV-PLELKKRKDAKQKAT 123 Query: 138 ARQLLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVREVL 197 +LL++V + ++ YP QLSGG+QQRV+IARA A +P+IL DEPT LD E + Sbjct: 124 --ELLQQVGLGDRMTHYPTQLSGGEQQRVSIARAFANEPKILFADEPTGNLDTETGELIE 181 Query: 198 DVMRDL-ASEGMTMLVATHEVGFAREVADRVVLMADGQIVEE 238 ++ DL + G T+++ TH+ A + +R++ + G+I EE Sbjct: 182 TLIFDLNKALGTTLILVTHDTDLAAK-TNRIIHIKGGKIQEE 222 Lambda K H 0.321 0.134 0.387 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: 126 Number of extensions: 6 Number of successful extensions: 3 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: 261 Length of database: 225 Length adjustment: 23 Effective length of query: 238 Effective length of database: 202 Effective search space: 48076 Effective search space used: 48076 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 (21.9 bits) S2: 46 (22.3 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