Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate WP_011385004.1 AMB_RS13205 polyamine ABC transporter ATP-binding protein
Query= reanno::pseudo5_N2C3_1:AO356_09610 (276 letters) >NCBI__GCF_000009985.1:WP_011385004.1 Length = 379 Score = 162 bits (409), Expect = 1e-44 Identities = 86/227 (37%), Positives = 132/227 (58%), Gaps = 6/227 (2%) Query: 43 GCVVGVNDLSLSIGTGEIFVIMGLSGSGKSTLVRHFNRLIDPTSGAILVDGEDILQLDMD 102 G V + L+I GE F ++G SG GK+TL+R PT+G IL+DG+D+ ++ Sbjct: 33 GDFTAVEHVDLAIHKGEFFSLLGASGCGKTTLLRMLAGFEIPTTGRILIDGQDVTEVPP- 91 Query: 103 ALREFRRHKISMVFQSFGLLPHKSVLDNVAYGLKVRGESKQVCAERALHWINTVGLKGYE 162 ++M+FQS+ L PH SV DN+A+GLK G +K V ++ + V + + Sbjct: 92 -----YERPVNMMFQSYALFPHMSVADNIAFGLKQDGLAKPVIKDKVAAALELVQMGRFS 146 Query: 163 NKYPHQLSGGMRQRVGLARALAADTDIILMDEAFSALDPLIRAEMQDQLLELQKTLHKTI 222 + PHQLSGG RQRV LAR LA + ++L+DE +ALD +R Q +L+ +Q + T Sbjct: 147 GRKPHQLSGGQRQRVALARCLAKEPKVVLLDEPLAALDKKLREATQLELVNIQDRVGITF 206 Query: 223 VFITHDLDEAVRIGNRIAILKDGKLIQVGTPREILHSPADEYVDRFV 269 V +THD EA+ + +RI ++ G + QVG+P +I P +V F+ Sbjct: 207 VMVTHDQGEAMTMSSRIGVMNAGCIEQVGSPVDIYEYPGTRFVADFI 253 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: 224 Number of extensions: 9 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: 379 Length adjustment: 28 Effective length of query: 248 Effective length of database: 351 Effective search space: 87048 Effective search space used: 87048 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