Align Putative ABC transporter arginine-binding protein 2 (characterized)
to candidate HSERO_RS17550 HSERO_RS17550 amino acid ABC transporter substrate-binding protein
Query= SwissProt::P30859 (243 letters) >FitnessBrowser__HerbieS:HSERO_RS17550 Length = 249 Score = 124 bits (312), Expect = 1e-33 Identities = 84/241 (34%), Positives = 125/241 (51%), Gaps = 7/241 (2%) Query: 3 KVLIAALIAGFSLSATA-AETIRFATEASYPPFESIDANNQIVGFDVDLAQALCKEIDAT 61 K++ A+L+A + A+A AET+ A + ++ PFE D NQ VGFD+DL A+ K+I T Sbjct: 7 KLVFASLVALSVVGASARAETLVVACDTAFVPFEFKD-RNQYVGFDIDLWDAIAKDIGVT 65 Query: 62 CTFSNQAFDSLIPSLKFRRVEAVMAGMDITPEREKQVLFTTPYYDNS-ALFVGQQGKYTS 120 F+ +IP+L+ + V+ +AG+ I ER+K + F+ YYD+ +L V S Sbjct: 66 YKLQPMDFNGIIPALQTKNVDVALAGITIKDERKKVIDFSDGYYDSGFSLMVPVGSSIKS 125 Query: 121 VDQLKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDGVFGDTAVVTE 180 V L GK + V++GT+ + + + NA L+LQ GR+D DT V Sbjct: 126 VADLAGKALAVKSGTSAFDYAKANFKATELHQFPNIDNAYLELQTGRVDAAMHDTPNVLY 185 Query: 181 WLKDNPKLAAVGDKVTDKDYFGTGLGIAVRQGNTELQQKLNTALEKVKKDGTYETIYNKW 240 ++ K A KV GI +G + L K+N AL K+K DG Y IY KW Sbjct: 186 YIATAGKGRA---KVVGTQMMAHQYGIGFPKG-SPLVPKVNAALAKIKADGRYAEIYRKW 241 Query: 241 F 241 F Sbjct: 242 F 242 Lambda K H 0.316 0.133 0.380 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: 155 Number of extensions: 13 Number of successful extensions: 4 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: 243 Length of database: 249 Length adjustment: 24 Effective length of query: 219 Effective length of database: 225 Effective search space: 49275 Effective search space used: 49275 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 (21.6 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