Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized)
to candidate Ga0059261_1321 Ga0059261_1321 ABC-type antimicrobial peptide transport system, ATPase component
Query= reanno::Smeli:SMc02121 (258 letters) >FitnessBrowser__Korea:Ga0059261_1321 Length = 238 Score = 119 bits (298), Expect = 6e-32 Identities = 80/223 (35%), Positives = 119/223 (53%), Gaps = 8/223 (3%) Query: 12 VSTTDVAIEITNMNKWYGD----FHVLRDINLRVMRGERIVVAGPSGSGKSTMIRCINRL 67 V+ D I + N+ K +G+ F L+ ++L + + + V GPSGSGKST + + L Sbjct: 1 VADADPIIRLRNITKVFGEGATAFQALKGVDLDIAERDFVAVMGPSGSGKSTTMNILGCL 60 Query: 68 EEHQKGKIVVDGIEL-TNDLKKIDEVRRE-VGMVFQHFNLFPHLTILENCTLAPIWVRKM 125 + G+ + G+ + T D + VRR+ +G VFQ FNL LEN L P+ R Sbjct: 61 DVPTSGEFLFKGVYIETLDRDQRALVRRKYLGFVFQGFNLLSRTNALENVEL-PLLYRGE 119 Query: 126 PKKEAEQVAMHFLERVKIPEQALKYPGQLSGGQQQRVAIARSLCMRPKILLFDEPTSALD 185 KK ++ M LE+V + + P +LSGGQ QRVAIAR++ P +LL DEPT LD Sbjct: 120 DKKVRHELGMAALEKVGLADWWDHTPAELSGGQPQRVAIARAIVTSPAVLLADEPTGNLD 179 Query: 186 PEMVKEVLDTMVGL-AEEGMTMICVTHEMGFARQVANRVIFMD 227 E+++ + L + G+T++ VTHE A V F D Sbjct: 180 SARSVEIMELLTSLNKDSGITVLMVTHEPDMAAFARTIVHFKD 222 Lambda K H 0.322 0.136 0.397 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: 129 Number of extensions: 8 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: 258 Length of database: 238 Length adjustment: 24 Effective length of query: 234 Effective length of database: 214 Effective search space: 50076 Effective search space used: 50076 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