Align ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component (characterized)
to candidate HSERO_RS17550 HSERO_RS17550 amino acid ABC transporter substrate-binding protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_3431 (257 letters) >FitnessBrowser__HerbieS:HSERO_RS17550 Length = 249 Score = 110 bits (274), Expect = 4e-29 Identities = 73/248 (29%), Positives = 134/248 (54%), Gaps = 12/248 (4%) Query: 3 KLVLLGALALSVLSLPTFADEKPLKIGIEAAYPPFASKAPDGSIVGFDYDIGNALCEEMK 62 KLV +ALSV+ A+ L + + A+ PF K + VGFD D+ +A+ +++ Sbjct: 7 KLVFASLVALSVVGASARAET--LVVACDTAFVPFEFKDRN-QYVGFDIDLWDAIAKDIG 63 Query: 63 VKCVWVEQEFDGLIPALKVRKIDAILSSMSITEDRKKSVDFTNKYYNTPARLVMKAGTAV 122 V +F+G+IPAL+ + +D L+ ++I ++RKK +DF++ YY++ L++ G+++ Sbjct: 64 VTYKLQPMDFNGIIPALQTKNVDVALAGITIKDERKKVIDFSDGYYDSGFSLMVPVGSSI 123 Query: 123 SENLAELKGKNIGVQRGSIHERFAREVLAPLGAEIKPYGSQNEIYLDVAAGRLDGTVADA 182 +++A+L GK + V+ G+ +A+ E+ + + + YL++ GR+D + D Sbjct: 124 -KSVADLAGKALAVKSGTSAFDYAKANFK--ATELHQFPNIDNAYLELQTGRVDAAMHDT 180 Query: 183 TLLDDGFLKTDAGKGFAFVGPAFTDVKYFGDGVGIAVRKGDALKDKINTAIAAIRENGKY 242 + + AGKG A V + GI KG L K+N A+A I+ +G+Y Sbjct: 181 P--NVLYYIATAGKGRAKV----VGTQMMAHQYGIGFPKGSPLVPKVNAALAKIKADGRY 234 Query: 243 KQIQDKYF 250 +I K+F Sbjct: 235 AEIYRKWF 242 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: 164 Number of extensions: 12 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: 249 Length adjustment: 24 Effective length of query: 233 Effective length of database: 225 Effective search space: 52425 Effective search space used: 52425 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: 46 (22.3 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