Align ABC transporter for L-Histidine, permease component 2 (characterized)
to candidate GFF2300 Psest_2346 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component
Query= reanno::acidovorax_3H11:Ac3H11_2561 (252 letters) >FitnessBrowser__psRCH2:GFF2300 Length = 296 Score = 99.0 bits (245), Expect = 1e-25 Identities = 61/198 (30%), Positives = 100/198 (50%) Query: 51 EYGFIKDIGMTIWRVVGGFVLAAVIAVPLGIAMGAYKGIEAFFEPFISFCRYLPASAFIP 110 +Y F +D ++ R+ G +AAV + LGIA G A P ++ +P A +P Sbjct: 93 DYLFWQDTASSLKRLGIGLAIAAVAGLCLGIAAGTLPLFSAPLSPLLTVLSMVPPLAILP 152 Query: 111 LLILWAGIGEAQKILVIFIGSVFQITLMVAVTVGGARRDLVEAAYTLGAGHKGIVTRVLI 170 +L + G+GE K+++I IG + + R+L+ A TLGA ++ R+++ Sbjct: 153 ILFIVFGLGELSKVMLIVIGITPILARDLEQRAREIPRELLIKAQTLGANTWTLILRLVL 212 Query: 171 PGAAPEIAETLRLVLGWAWTYVIVAELIGSSSGIGHMITDSQSLLNTGQIIFGIIIIGLI 230 P P + +LRLVLG AW ++I AE I S+ G+G+ I + + I+ + I L+ Sbjct: 213 PQLMPRLLISLRLVLGSAWLFLIAAEAIASTDGLGYRIFLVRRYMAMDVILPYVAWITLL 272 Query: 231 GLVSDFAFKALNHRLFAW 248 DF + L LF W Sbjct: 273 AWAMDFTLRRLTQLLFPW 290 Lambda K H 0.331 0.145 0.456 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: 185 Number of extensions: 12 Number of successful extensions: 3 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: 252 Length of database: 296 Length adjustment: 25 Effective length of query: 227 Effective length of database: 271 Effective search space: 61517 Effective search space used: 61517 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 47 (22.7 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