Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate Ga0059261_1321 Ga0059261_1321 ABC-type antimicrobial peptide transport system, ATPase component
Query= reanno::pseudo6_N2E2:Pf6N2E2_5405 (254 letters) >FitnessBrowser__Korea:Ga0059261_1321 Length = 238 Score = 129 bits (325), Expect = 4e-35 Identities = 82/214 (38%), Positives = 123/214 (57%), Gaps = 11/214 (5%) Query: 14 IIQMQGVNKWYGQ----FHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQG 69 II+++ + K +G+ F LK ++L++ + + + + GPSGSGKSTT+ L L+ G Sbjct: 7 IIRLRNITKVFGEGATAFQALKGVDLDIAERDFVAVMGPSGSGKSTTMNILGCLDVPTSG 66 Query: 70 RIVVDGVEL-TNDLKQIEAIRRE-VGMVFQHFNLFPHLTILQNCTLAPMWVRKMPKRKAE 127 + GV + T D Q +RR+ +G VFQ FNL L+N L P+ R K+ Sbjct: 67 EFLFKGVYIETLDRDQRALVRRKYLGFVFQGFNLLSRTNALENVEL-PLLYRGEDKKVRH 125 Query: 128 EIAMHYLERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVKE 187 E+ M LE+V + + P +LSGGQ QRVAIARA+ P ++L DEPT LD E Sbjct: 126 ELGMAALEKVGLADWWDHTPAELSGGQPQRVAIARAIVTSPAVLLADEPTGNLDSARSVE 185 Query: 188 VLDTMIGLAED-GMTMLCVTHE---MGFARTVAN 217 +++ + L +D G+T+L VTHE FART+ + Sbjct: 186 IMELLTSLNKDSGITVLMVTHEPDMAAFARTIVH 219 Lambda K H 0.322 0.137 0.407 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: 142 Number of extensions: 9 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 254 Length of database: 238 Length adjustment: 24 Effective length of query: 230 Effective length of database: 214 Effective search space: 49220 Effective search space used: 49220 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