Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate Echvi_2123 Echvi_2123 ABC-type spermidine/putrescine transport systems, ATPase components
Query= reanno::pseudo5_N2C3_1:AO356_09610 (276 letters) >FitnessBrowser__Cola:Echvi_2123 Length = 318 Score = 134 bits (337), Expect = 3e-36 Identities = 71/222 (31%), Positives = 132/222 (59%), Gaps = 4/222 (1%) Query: 46 VGVNDLSLSIGTGEIFVIMGLSGSGKSTLVRHFNRLIDPTSGAILVDGEDILQLDMDALR 105 + + D SL + G + ++G SGSGKS+L+R L ++G + + + IL + Sbjct: 18 LALEDFSLQVKRGGVVSMVGESGSGKSSLLRIIAGLEVQSAGVVHLGDQKILNPAQKLVP 77 Query: 106 EFRRHKISMVFQSFGLLPHKSVLDNVAYGLKVRGESKQVCAERALHWINTVGLKGYENKY 165 + +I ++ Q + L P+ +V +N+A L + ++ Q ER + + L+ +++K Sbjct: 78 GY--DEIQLIHQEYKLYPNSTVEENIARPLLLYDKAYQ--KERTAEILELLSLRAFKDKK 133 Query: 166 PHQLSGGMRQRVGLARALAADTDIILMDEAFSALDPLIRAEMQDQLLELQKTLHKTIVFI 225 P QLSGG +Q+V + RAL+ + +++L+DE FS+LD + + ++ ++L E+ L T++F+ Sbjct: 134 PRQLSGGQQQKVAIGRALSIEPEVLLLDEPFSSLDAIQKRDLIEELKEIFDALEVTVIFV 193 Query: 226 THDLDEAVRIGNRIAILKDGKLIQVGTPREILHSPADEYVDR 267 THD+D+A+ + + I++ GKL+Q G RE+ PA YV R Sbjct: 194 THDVDDALLMSEELLIIQKGKLLQQGNVREVFRKPASAYVAR 235 Lambda K H 0.321 0.138 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: 188 Number of extensions: 14 Number of successful extensions: 2 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: 276 Length of database: 318 Length adjustment: 26 Effective length of query: 250 Effective length of database: 292 Effective search space: 73000 Effective search space used: 73000 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: 48 (23.1 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