Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate YP_004144287.1 Mesci_5138 glycine betaine/L-proline ABC transporter ATPase
Query= reanno::pseudo5_N2C3_1:AO356_09610 (276 letters) >NCBI__GCF_000185905.1:YP_004144287.1 Length = 361 Score = 265 bits (677), Expect = 1e-75 Identities = 134/263 (50%), Positives = 185/263 (70%), Gaps = 1/263 (0%) Query: 8 KIEVKNVFKIFGNRSKEALELIRQNKTKDQVLAETGCVVGVNDLSLSIGTGEIFVIMGLS 67 K+ +NV+K+FG+ + + R K + G V V + L I GEIF+IMGLS Sbjct: 22 KLACRNVWKLFGSNAANFIRE-RDGKASMADVTAAGLVGAVRAVDLEIRQGEIFIIMGLS 80 Query: 68 GSGKSTLVRHFNRLIDPTSGAILVDGEDILQLDMDALREFRRHKISMVFQSFGLLPHKSV 127 GSGKSTLVR +RL++PT G + +G D+L++ AL E RRH++ MVFQ+F LLPH +V Sbjct: 81 GSGKSTLVRCMSRLVEPTHGKVEFEGNDLLKISDAALIELRRHRMGMVFQNFALLPHLNV 140 Query: 128 LDNVAYGLKVRGESKQVCAERALHWINTVGLKGYENKYPHQLSGGMRQRVGLARALAADT 187 L+N+A+ L ++G+ + RA I VGL+G E+ YP +LSGG +QRVG+AR+LA Sbjct: 141 LENIAFPLSIQGQDRATREARAREVIELVGLRGREHFYPRELSGGQQQRVGIARSLATKP 200 Query: 188 DIILMDEAFSALDPLIRAEMQDQLLELQKTLHKTIVFITHDLDEAVRIGNRIAILKDGKL 247 +I +DE FSALDPLIR EMQD+L+ LQ LHKTIVFITHD DEA+R+ +RIAI+KDG++ Sbjct: 201 EIWFLDEPFSALDPLIRREMQDELMRLQMMLHKTIVFITHDFDEAIRLADRIAIMKDGEV 260 Query: 248 IQVGTPREILHSPADEYVDRFVQ 270 IQ+GTP E++ +PA +YV F + Sbjct: 261 IQIGTPEELVVNPATDYVAEFTR 283 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: 272 Number of extensions: 12 Number of successful extensions: 1 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: 361 Length adjustment: 27 Effective length of query: 249 Effective length of database: 334 Effective search space: 83166 Effective search space used: 83166 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 24 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