Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate GFF960 HP15_939 spermidine/putrescine ABC transporter ATPase subunit
Query= reanno::pseudo5_N2C3_1:AO356_09610 (276 letters) >FitnessBrowser__Marino:GFF960 Length = 372 Score = 161 bits (407), Expect = 2e-44 Identities = 88/224 (39%), Positives = 136/224 (60%), Gaps = 6/224 (2%) Query: 46 VGVNDLSLSIGTGEIFVIMGLSGSGKSTLVRHFNRLIDPTSGAILVDGEDILQLDMDALR 105 + V++++L I GEIF ++G SGSGKSTL+R P +G+I++DG+D+ AL Sbjct: 28 LAVDNVNLDIHKGEIFALLGGSGSGKSTLLRMLAGFETPNAGSIMLDGQDVT-----ALP 82 Query: 106 EFRRHKISMVFQSFGLLPHKSVLDNVAYGLKVRGESKQVCAERALHWINTVGLKGYENKY 165 F R +M+FQS+ L PH +V N+A GLK K +R + V ++ Y + Sbjct: 83 PFLR-PTNMMFQSYALFPHMTVEQNIAMGLKQDKLPKSEIRDRVAAMLKLVKMEPYARRK 141 Query: 166 PHQLSGGMRQRVGLARALAADTDIILMDEAFSALDPLIRAEMQDQLLELQKTLHKTIVFI 225 P QLSGG +QRV LAR+LA ++L+DE ALD +R EMQ +L+E+ + + T + + Sbjct: 142 PQQLSGGQQQRVALARSLAKRPKLLLLDEPMGALDKKLRTEMQLELVEILENVGATCLMV 201 Query: 226 THDLDEAVRIGNRIAILKDGKLIQVGTPREILHSPADEYVDRFV 269 THD +EA+ + +RIAI+ G++ Q+G+P +I SP F+ Sbjct: 202 THDQEEAMTMASRIAIMAQGRIAQIGSPIDIYESPNSRMTAEFI 245 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: 203 Number of extensions: 11 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: 372 Length adjustment: 28 Effective length of query: 248 Effective length of database: 344 Effective search space: 85312 Effective search space used: 85312 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