Align Xylose ABC transporter, periplasmic xylose-binding protein XylF (characterized, see rationale)
to candidate Ac3H11_2879 Ribose ABC transporter, periplasmic ribose-binding protein RbsB (TC 3.A.1.2.1)
Query= uniprot:A0A0C4Y591 (325 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2879 Length = 325 Score = 114 bits (286), Expect = 2e-30 Identities = 97/318 (30%), Positives = 154/318 (48%), Gaps = 17/318 (5%) Query: 11 TAALSLLCTGAAAQSAPDAAPASAAAQRPLKKVGVTLGSLGNPYFVALAHGAEAAAK--- 67 T L+L GAAA + AAPA A A + + VGV + S + + + + A A K Sbjct: 8 TRRLALSAVGAAAFAL--AAPAMAQANKTV--VGVAIPSATHGFTGGIVYWANQAKKDLE 63 Query: 68 KINPDAKVTVLSADYDLNKQFSHIDSFIVSKVDLILINAADARAIEPAVRKARKAGIVVV 127 K +P +V V +A + D V+K++ ++I ++ A+ V + + G+ V Sbjct: 64 KAHPGLQVIVKTAGGAPEQANQLQDLVTVNKINALVIFPFESAALTKPVAQVKAKGVYVT 123 Query: 128 AVD---VAAAGADATVQTDNTRAGELACAFLAGRLGGRGNLIIQNGPPVSAVLDRVKGCK 184 VD + DA V DNT G++ ++A LGG+GN++ G + +R+ Sbjct: 124 VVDRGLTDTSAQDAYVAGDNTAFGKIPAEYIAKALGGKGNVVAMRGIATTLDNERMDAFN 183 Query: 185 MVLGKHPGIHVLSDDQDGKGSREGGLNVMQLYLTRFPKIDAVFTINDPQAVGADLAARQL 244 VL HPGI +L D + +R+ VMQ YLTRFP+IDAV+ +D AVG A Q Sbjct: 184 SVLKNHPGIKLL-DAKYANWNRDDAFKVMQDYLTRFPQIDAVWAADDDMAVGVLKAIEQA 242 Query: 245 NRGGI-LIASVDGAPDIEAALK--ANTLVQASASQDPWAIARTAVEIGVGLMHGQ-APAN 300 R I L+ GA + L +N ++QA+ S P I + + G+ PAN Sbjct: 243 KRKDIKLVFGGAGAKGMIKTLMDGSNPMIQANVSYSPKFIYDSIKLTAEARIKGEKLPAN 302 Query: 301 RTVLLPPTLVTRANVNEY 318 ++P L+T+ ++ Sbjct: 303 --TIIPSVLITKETAKDF 318 Lambda K H 0.318 0.132 0.377 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: 199 Number of extensions: 10 Number of successful extensions: 2 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: 325 Length of database: 325 Length adjustment: 28 Effective length of query: 297 Effective length of database: 297 Effective search space: 88209 Effective search space used: 88209 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: 48 (23.1 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