Align Putative ABC transporter arginine-binding protein 2 (characterized)
to candidate GFF2974 HP15_2918 glutamine ABC transporter, periplasmic glutamine-binding protein
Query= SwissProt::P30859 (243 letters) >FitnessBrowser__Marino:GFF2974 Length = 252 Score = 120 bits (302), Expect = 2e-32 Identities = 79/247 (31%), Positives = 130/247 (52%), Gaps = 16/247 (6%) Query: 3 KVLIAALIAGFSLSATAAETIRFATEASYPPFESIDANN-QIVGFDVDLAQALCKEIDAT 61 K + A+L + +AET+R T+ S+ PFE +D +++GFD+++ + + Sbjct: 7 KTVSASLALTVAAGTVSAETLRVVTDPSFVPFEMMDQETGEMIGFDMEIIREVADRAGFE 66 Query: 62 CTFSNQAFDSLIPSLKFRRVEAVMAGMDITPEREKQVLFTTPYYDNSALFVGQQGK--YT 119 + F+ +IP+L+ V+ +AG+ IT ERE+ V F+ PYYD+ + ++G + Sbjct: 67 IDLNTMDFNGIIPALQTGNVDIAIAGITITEEREEIVDFSDPYYDSGLRILVREGNDDVS 126 Query: 120 SVDQLKGKKVGVQNGTTHQKFI---MDKHPEITTVPYDSYQNAKLDLQNGRIDGVFGDTA 176 D L+GKK+G + G+T ++ +D +T PY + + L + ID VF D Sbjct: 127 EFDDLEGKKIGTKIGSTSYDYLVKNLDADDGVT--PYPGSSDMYMALMSRAIDAVFYDAP 184 Query: 177 VVTEW--LKDNPKLAAVGDKVTDKDYFGTGLGIAVRQGNTELQQKLNTALEKVKKDGTYE 234 V + K K+ VG Y G GIA++ G +E +N AL +K+DGTY+ Sbjct: 185 NVGYFARTKGEGKVTTVGPL-----YEGQQYGIALKSG-SEWVDDVNEALAAMKEDGTYK 238 Query: 235 TIYNKWF 241 TIY KWF Sbjct: 239 TIYEKWF 245 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: 187 Number of extensions: 13 Number of successful extensions: 5 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: 252 Length adjustment: 24 Effective length of query: 219 Effective length of database: 228 Effective search space: 49932 Effective search space used: 49932 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