Align ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component (characterized)
to candidate BWI76_RS20340 BWI76_RS20340 histidine ABC transporter substrate-binding protein HisJ
Query= reanno::pseudo1_N1B4:Pf1N1B4_3431 (257 letters) >FitnessBrowser__Koxy:BWI76_RS20340 Length = 260 Score = 229 bits (584), Expect = 4e-65 Identities = 116/260 (44%), Positives = 166/260 (63%), Gaps = 3/260 (1%) Query: 1 MKKLVLLGALALSVLSLPTFADEKP--LKIGIEAAYPPFASKAPDGSIVGFDYDIGNALC 58 MKK VL +L + + S + P ++IG +A Y PF+SK G VGFD D+GN LC Sbjct: 1 MKKTVLALSLMMGICSASSAFAALPQSIRIGTDATYAPFSSKDAKGDFVGFDIDLGNELC 60 Query: 59 EEMKVKCVWVEQEFDGLIPALKVRKIDAILSSMSITEDRKKSVDFTNKYYNTPARLVMKA 118 +KVKC WV +FD LIP+LK +KIDAI+SS+SITE R++ + F++K Y +RL+ Sbjct: 61 SRIKVKCTWVGSDFDSLIPSLKAKKIDAIISSLSITEKRQQEIAFSDKLYAADSRLIAAK 120 Query: 119 GTAVSENLAELKGKNIGVQRGSIHERFAREVLAPLGAEIKPYGSQNEIYLDVAAGRLDGT 178 G+ + L LKGK++GV +GS E + E G ++ Y +Q+ IY D++AGRLD Sbjct: 121 GSPIQPTLESLKGKHVGVLQGSTQEAYGNERWRSHGVDVVAYQNQDLIYSDLSAGRLDAA 180 Query: 179 VADATLLDDGFLKTDAGKGFAFVGPAFTDVKYFGDGVGIAVRKGDA-LKDKINTAIAAIR 237 + D +GFLK AGK FAF GP+ D K+FGDG GI +RK D+ LK + A+A +R Sbjct: 181 LQDEVAASEGFLKQPAGKDFAFAGPSVKDKKFFGDGTGIGLRKDDSELKAAFDKALADMR 240 Query: 238 ENGKYKQIQDKYFAFDIYGK 257 ++G Y ++ KYF F++YG+ Sbjct: 241 KDGTYDKMAKKYFDFNVYGE 260 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: 218 Number of extensions: 10 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