Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate Echvi_1582 Echvi_1582 ABC-type antimicrobial peptide transport system, ATPase component
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >FitnessBrowser__Cola:Echvi_1582 Length = 225 Score = 145 bits (367), Expect = 5e-40 Identities = 90/229 (39%), Positives = 135/229 (58%), Gaps = 17/229 (7%) Query: 1 MSSVSIQAVSRVFETAKGQRT-QALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDH 59 M +SI+ VS+++++ G RT L+ ++ V+ D + I+GPSG GK+TLL + AGLD Sbjct: 1 MDILSIENVSKIYQS--GSRTLTVLEDINLSVKAGDSIAIVGPSGSGKTTLLGLCAGLDS 58 Query: 60 ATSGRVLLDGAPVEGPGAER---------GMVFQSYTLFPWLTIEQNIRFGLRERGMPEA 110 A+SG V L+G +EG ++ G +FQ++ L P LT +N+ L + +A Sbjct: 59 ASSGSVALNGHRLEGLSEDQRAAVRSQEIGFIFQNFQLLPTLTALENVMVPLELKKRKDA 118 Query: 111 QQKERAAYFIAKVGLRGFEQHFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQT 170 +QK A + +VGL H+P QLSGG QQR +IARA AN+PKIL DEP G LD +T Sbjct: 119 KQK--ATELLQQVGLGDRMTHYPTQLSGGEQQRVSIARAFANEPKILFADEPTGNLDTET 176 Query: 171 RVLMQELLLGIWEAERKTVLFVTHDIDEAIFMANRVAVFSARPGRIKTE 219 L++ L+ + +A T++ VTHD D A A + + G+I+ E Sbjct: 177 GELIETLIFDLNKALGTTLILVTHDTDLA---AKTNRIIHIKGGKIQEE 222 Lambda K H 0.322 0.136 0.394 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: 3 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: 259 Length of database: 225 Length adjustment: 23 Effective length of query: 236 Effective length of database: 202 Effective search space: 47672 Effective search space used: 47672 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