Align TRAP-type periplasmic solute-binding protein (characterized, see rationale)
to candidate AZOBR_RS26640 AZOBR_RS26640 ABC transporter substrate-binding protein
Query= uniprot:Q930R1 (334 letters) >FitnessBrowser__azobra:AZOBR_RS26640 Length = 339 Score = 370 bits (950), Expect = e-107 Identities = 177/330 (53%), Positives = 241/330 (73%), Gaps = 1/330 (0%) Query: 5 LLATTAIAFGLSAAAPAFAEFNDRNIRVSNGINEDHPVGNGIKAMQACLDQKSGGKLKLT 64 ++ T A+A L AAAPA A+ +R +R+S + +DHP G+ A+ AC +KSGGK+K+ Sbjct: 8 IILTVAVA-ALFAAAPAKAQTAERTMRLSAAVAQDHPFAAGVSALTACAAEKSGGKMKIQ 66 Query: 65 AFWGGALGGDLQATQALRSGVQEAVVTSSSPLVGIIPALGVFDLPFLFANAQEAYTVLDG 124 +FW ALG D+QA Q +R G + VV S+SPL ++PA+GVFDLPFLF N EA +LDG Sbjct: 67 SFWNAALGSDMQAVQLVRGGSLDMVVASTSPLASLVPAMGVFDLPFLFENETEADRILDG 126 Query: 125 DFGDMMNEKLEAAGLVNLAYWENGFRNLSNSVRPVTKWEDFEGMKVRVMQNNIFLDTFQN 184 G ++EKL+ GLVNLAYWENGFRNL+NS RP+ KWED G K+RVMQN +F+DTF Sbjct: 127 AVGQQLSEKLQGVGLVNLAYWENGFRNLTNSRRPIQKWEDLGGTKIRVMQNPVFMDTFST 186 Query: 185 LGANATPMAFGEVFSALETKAIDAQENPYVTIDTSKFFEVQKYVTETNHAYTPFLFLFSK 244 LGANA PMAF E+F+ALET+A+D QENPY I+T KF+E QKY++ TNHAYTP + L+SK Sbjct: 187 LGANAVPMAFSELFTALETRAVDGQENPYANIETGKFYEAQKYLSVTNHAYTPAVILYSK 246 Query: 245 PIFDSYTPEEQAALRECAVVGRDEERKVIQDLNKKSLEKIKEAGLEVNTLSAEEQARIRE 304 I+D + E+ L+ CA V R EER+V ++ ++KSL ++K+ G++VN LSAEE+ R+ + Sbjct: 247 KIWDGLSSAERDVLQSCAAVARTEERRVNREQSEKSLARLKDLGMQVNELSAEERKRMLQ 306 Query: 305 KSMVVYEKHKAEIGAEVVDAILAKLEEIRK 334 K VYEKH A IGAE + + ++L ++RK Sbjct: 307 KVAPVYEKHAATIGAETMTLLQSELGQLRK 336 Lambda K H 0.317 0.133 0.374 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: 305 Number of extensions: 13 Number of successful extensions: 1 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: 334 Length of database: 339 Length adjustment: 28 Effective length of query: 306 Effective length of database: 311 Effective search space: 95166 Effective search space used: 95166 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: 49 (23.5 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