Align ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component (characterized)
to candidate BWI76_RS20335 BWI76_RS20335 zinc transporter
Query= reanno::pseudo1_N1B4:Pf1N1B4_3431 (257 letters) >FitnessBrowser__Koxy:BWI76_RS20335 Length = 260 Score = 219 bits (558), Expect = 4e-62 Identities = 112/259 (43%), Positives = 164/259 (63%), Gaps = 3/259 (1%) Query: 1 MKKLVLLGALALSVLSLPTF--ADEKPLKIGIEAAYPPFASKAPDGSIVGFDYDIGNALC 58 MKKL L +LAL++ S+ T A + ++IG + Y PF SK G +VGFD D+ LC Sbjct: 1 MKKLALSLSLALALSSVSTVFAAIPQKVRIGTDPTYAPFESKNAQGELVGFDIDLAKELC 60 Query: 59 EEMKVKCVWVEQEFDGLIPALKVRKIDAILSSMSITEDRKKSVDFTNKYYNTPARLVMKA 118 + + +C ++E D LIP+LK +KIDAI+SS+SITE R++ + FT+K Y +RLV+K Sbjct: 61 KRINTQCTFIENPLDALIPSLKAKKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLVVKK 120 Query: 119 GTAVSENLAELKGKNIGVQRGSIHERFAREVLAPLGAEIKPYGSQNEIYLDVAAGRLDGT 178 G+ ++ +LA+LKGK +GV +G+ E + E AP G EI Y Q+ IY D+ AGR+D Sbjct: 121 GSDITPDLAKLKGKRVGVLQGTTQETYGNEHWAPKGIEIVSYQGQDNIYSDLTAGRIDAA 180 Query: 179 VADATLLDDGFLKTDAGKGFAFVGPAFTDVKYFGDGVGIAVRKGD-ALKDKINTAIAAIR 237 D +GFLK GK + F GP+ D K FG G G+ +RK D L++ +N A A +R Sbjct: 181 FQDEVAASEGFLKQPIGKDYQFGGPSIKDEKLFGVGTGMGLRKEDNELREALNKAFAEMR 240 Query: 238 ENGKYKQIQDKYFAFDIYG 256 ++G Y ++ KYF F++YG Sbjct: 241 QDGTYDKLAKKYFDFNVYG 259 Lambda K H 0.318 0.138 0.394 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: 187 Number of extensions: 6 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: 257 Length of database: 260 Length adjustment: 24 Effective length of query: 233 Effective length of database: 236 Effective search space: 54988 Effective search space used: 54988 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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