Align Extracellular solute-binding protein family 3; Flags: Precursor (characterized, see rationale)
to candidate AZOBR_RS27130 AZOBR_RS27130 polyamine ABC transporter substrate-binding protein
Query= uniprot:B2TBJ6 (286 letters) >FitnessBrowser__azobra:AZOBR_RS27130 Length = 259 Score = 186 bits (473), Expect = 4e-52 Identities = 106/277 (38%), Positives = 152/277 (54%), Gaps = 26/277 (9%) Query: 13 IGAVLGAAAIFAA--PAQAKDWKTVTIALEGGYAPWNLTLPGGKLGGFEPELVANLCERI 70 +G +G A+ AA A D + IA EG Y P+N+T P G LGG E EL LCERI Sbjct: 6 LGLAMGLCALAAAVPTASRADGPPLRIATEGAYPPFNMTSPDGTLGGLEVELANALCERI 65 Query: 71 KLQCNLVAQDWDGMIPGLQAGKFDVLMDAISITPEREKIIAFSKPYAATPATFAVADAKV 130 K +C LVAQDWDG+IPGL + ++D +M ++ITPER K IAFS PY PA F Sbjct: 66 KRRCTLVAQDWDGIIPGLLSRRYDAIMATMNITPERAKAIAFSAPYMVVPAYFV------ 119 Query: 131 LPKAAPGAGVVKLSGDPKADQPTVDALRKQLKGKTIGIQSGTVYTKFINDGFKDIATIRV 190 AA G G +D L GK++G Q+ T + +++ F +++ Sbjct: 120 ---AATGGG--------------IDGTEATLAGKSVGAQTSTTHYRYVEKHFGKTVSLKN 162 Query: 191 YKTSPERDLDLANGRIDASFDDVTYYAANIDKKETASIVMAG-PKIGGPIWGPGEGLAFR 249 Y T+ DL +GRIDA+ + + + S+ + G P + ++GPG G+ R Sbjct: 163 YDTASNLLADLKSGRIDAAITTGATASDWVKADASKSLQLVGKPLVDAEVFGPGVGVGLR 222 Query: 250 KQDADLKAKFDTAISAALADGTVKKLSNKWFKTDVTP 286 K+DADLKA FD AI++ + DGT+ +++ K+ VTP Sbjct: 223 KEDADLKAAFDAAIASVVQDGTLARIAAKYVDFTVTP 259 Lambda K H 0.316 0.134 0.396 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: 204 Number of extensions: 9 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: 286 Length of database: 259 Length adjustment: 25 Effective length of query: 261 Effective length of database: 234 Effective search space: 61074 Effective search space used: 61074 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: 47 (22.7 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