Align ABC transporter for L-Histidine, periplasmic substrate-binding component 1 (characterized)
to candidate GFF2974 HP15_2918 glutamine ABC transporter, periplasmic glutamine-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_2555 (249 letters) >FitnessBrowser__Marino:GFF2974 Length = 252 Score = 130 bits (326), Expect = 3e-35 Identities = 77/236 (32%), Positives = 123/236 (52%), Gaps = 6/236 (2%) Query: 13 AAAAFCTTGAQAQDNVLRVGTDATFPPMEFV--ENGKRTGFDIELVEAIAKTMGKQVEWV 70 A+ A LRV TD +F P E + E G+ GFD+E++ +A G +++ Sbjct: 11 ASLALTVAAGTVSAETLRVVTDPSFVPFEMMDQETGEMIGFDMEIIREVADRAGFEIDLN 70 Query: 71 DIDFKGLIPGLISKRFDMAVSAIYITDERKKVVDFTDSYYAGGLVVMVKADNKAINKLAD 130 +DF G+IP L + D+A++ I IT+ER+++VDF+D YY GL ++V+ N +++ D Sbjct: 71 TMDFNGIIPALQTGNVDIAIAGITITEEREEIVDFSDPYYDSGLRILVREGNDDVSEFDD 130 Query: 131 LDGKKVSVQVGTKSVSYLTEKFPKVQRVEVEKNQEMFNLVDIGRA-DAAVTGKPAAFQYV 189 L+GKK+ ++G+ S YL + V + + RA DA P + Sbjct: 131 LEGKKIGTKIGSTSYDYLVKNLDADDGVTPYPGSSDMYMALMSRAIDAVFYDAPNVGYFA 190 Query: 190 RTRPGLRV--LDEQLTTEEYGMALRKDTPELTKAVNGAITKLKADGTYAAIVKKWF 243 RT+ +V + ++YG+AL K E VN A+ +K DGTY I +KWF Sbjct: 191 RTKGEGKVTTVGPLYEGQQYGIAL-KSGSEWVDDVNEALAAMKEDGTYKTIYEKWF 245 Lambda K H 0.317 0.133 0.369 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: 162 Number of extensions: 12 Number of successful extensions: 3 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: 249 Length of database: 252 Length adjustment: 24 Effective length of query: 225 Effective length of database: 228 Effective search space: 51300 Effective search space used: 51300 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