Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate AZOBR_RS25645 AZOBR_RS25645 amino acid ABC transporter substrate-binding protein
Query= uniprot:A0A165KTD4 (375 letters) >FitnessBrowser__azobra:AZOBR_RS25645 Length = 370 Score = 146 bits (368), Expect = 1e-39 Identities = 116/379 (30%), Positives = 179/379 (47%), Gaps = 22/379 (5%) Query: 5 LKLTVVAAI--AAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGV 62 LK +AA+ A AG A A + VKIG+ P++G A YG+D A +A+ E NA G Sbjct: 4 LKTASLAALMTGALAGTALAAD-TVKIGYQLPLTGETAQYGQDFRKAAEIALTEFNASG- 61 Query: 63 TIGGKKIKFELVAEDDAADPKQGTAAAQKLCDAK-VAGVVGHLNSGTTIPASKVYNDCGI 121 K K E+V ED +D K+GT A+K D K + GV+G SG ++ +++VY D G+ Sbjct: 62 ----KPFKAEIVFEDSRSDAKEGTNIARKFVDDKAIVGVLGDFTSGVSMASAQVYKDAGM 117 Query: 122 PHVTGAATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGV 181 P ++ A++P+ TK K FR IA G A + + K +A+I ++T +GQ V Sbjct: 118 PQLSQTASHPDYTKIS-KYQFRNIATQAQEGPYNAKWMLSK-GYKNIAVIAEQTDWGQSV 175 Query: 182 ADVFKKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQME 241 F A G VV +F D+ ++++ ++ PDAI+ G G LRQ++ Sbjct: 176 VSGFTDGVKANGGTVVFSEFFNRGLKDYRSLISKLERAKPDAIYTGFFYEDGAQFLRQVQ 235 Query: 242 QLGMGNVKYFGGDGICTSEI---AKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDA 298 QLG+ Y I + A G N + + + T WKA + Sbjct: 236 QLGIKTPVYSTSAAYSPKLIELAGEAAEGVHLTSNFLPTDPAPHIQHFV--TEWKAASNG 293 Query: 299 KYPNQFQVYSPYTYDATFLIVDAMKRA--NSVDPKVYTPELAKSSFKGVTSTIAFEPNGE 356 P QF + YDA +++ A+++A N KV F GVT +F + E Sbjct: 294 AVPGQFPAQA---YDAVRIMLAAVEKAYPNPTREKVRDALAETKDFPGVTGKTSFSADRE 350 Query: 357 MKNPAITLYVYKDGKKTPL 375 + + + V K G P+ Sbjct: 351 AEKELVKVEV-KGGAFVPV 368 Lambda K H 0.315 0.131 0.375 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: 329 Number of extensions: 18 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: 375 Length of database: 370 Length adjustment: 30 Effective length of query: 345 Effective length of database: 340 Effective search space: 117300 Effective search space used: 117300 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: 42 (22.0 bits) S2: 50 (23.9 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