Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate SMc04439 SMc04439 glycine betaine transport ATP-binding ABC transporter protein
Query= reanno::pseudo5_N2C3_1:AO356_09610 (276 letters) >FitnessBrowser__Smeli:SMc04439 Length = 297 Score = 282 bits (721), Expect = 7e-81 Identities = 136/213 (63%), Positives = 175/213 (82%) Query: 58 GEIFVIMGLSGSGKSTLVRHFNRLIDPTSGAILVDGEDILQLDMDALREFRRHKISMVFQ 117 G I V+MGLSGSGKSTL+RH NRLIDPTSG +L DG D+ +++ + LR FRRHK +MVFQ Sbjct: 4 GCITVVMGLSGSGKSTLIRHINRLIDPTSGEVLYDGVDVCKMNENDLRAFRRHKTAMVFQ 63 Query: 118 SFGLLPHKSVLDNVAYGLKVRGESKQVCAERALHWINTVGLKGYENKYPHQLSGGMRQRV 177 F LLPH++VL+N YGL+++G ++ +RAL WI VGL+G+E YP+QLSGGM+QRV Sbjct: 64 KFALLPHRTVLENTIYGLEIQGVDRRESEKRALGWIERVGLQGFEKHYPNQLSGGMQQRV 123 Query: 178 GLARALAADTDIILMDEAFSALDPLIRAEMQDQLLELQKTLHKTIVFITHDLDEAVRIGN 237 GLARAL D DI+LMDEA+SALDPLIR +MQ LLELQK L KT+VFITHDLDEA+R+G+ Sbjct: 124 GLARALTNDADILLMDEAYSALDPLIRVDMQSVLLELQKELKKTVVFITHDLDEALRLGD 183 Query: 238 RIAILKDGKLIQVGTPREILHSPADEYVDRFVQ 270 +IAIL+DG+++Q GT +EI+ SPAD+Y+ FV+ Sbjct: 184 KIAILRDGRVVQQGTGQEIVLSPADDYITAFVK 216 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: 260 Number of extensions: 11 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: 297 Length adjustment: 26 Effective length of query: 250 Effective length of database: 271 Effective search space: 67750 Effective search space used: 67750 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: 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