Align L-rhamnonate dehydratase; RhamD; EC 4.2.1.90 (characterized)
to candidate AZOBR_RS04900 AZOBR_RS04900 dehydratase
Query= SwissProt::Q12DF1 (395 letters) >FitnessBrowser__azobra:AZOBR_RS04900 Length = 386 Score = 122 bits (305), Expect = 2e-32 Identities = 107/368 (29%), Positives = 168/368 (45%), Gaps = 52/368 (14%) Query: 57 LGTLVVEIEASDGTVGFS-VTTGGELG----CWIVEKHLARFIEGAKVTDIEKIWDQMFN 111 L ++V+++ +G G V T G +++ ARF+ GA T I + +M++ Sbjct: 16 LKPVIVKLDTDEGISGLGEVATAYGCGRTGAAGMIQDLCARFVIGADPTRINSLVGEMYD 75 Query: 112 ATLYYGRKGIVLNT-ISGVDLALWDLLAKVRKEPVHALLGGPVRDELTFYATG------- 163 + + G + +S ++ ALWD+ A+ PVH L GG +RD L +YA G Sbjct: 76 QSFWLKNPGGIAGAGLSAIEQALWDIRARALNVPVHELFGGRMRDTLAYYANGWYFGATS 135 Query: 164 -----ARPDLAKKMGFIGGKL----------PLHHGP---AEREEGLKKNLELLGEMRQR 205 + + A K G K+ L H A+ + + L+++ ++R+ Sbjct: 136 VADLLRQAEAAVKDGHKALKMYPLARIQPNGTLRHTVNRYADDRDAVNAALDIVAQVRRT 195 Query: 206 VGDDFWLMYDCWMSLDVEYATRLANAASEYKLKWIEEALPPDDYWGYAEL--RRNVPRGM 263 VG D LM D V R + + + +IEE P D ++ + N+P Sbjct: 196 VGADVTLMLDLAGGFSVSDTIRFVHGLEDLDIAFIEEICDPGDLGALEQVAAKTNIP--- 252 Query: 264 LVTTGEHEATRWGFRMLLEMECCDILQPDVGWCGGITELLKISALADAHGKLVVPH--GS 321 + TGE + R+GFR LLE ILQPD+G GG E KI+A+ADA+G V PH GS Sbjct: 253 -IATGERQYLRYGFRDLLERRAVGILQPDIGNTGGFAETHKIAAMADAYGVKVQPHVCGS 311 Query: 322 SVYSYHFVITRHNSPFSEFLMMAPKADEVVPMFN--PMLLDEPV-PVNGRMKASAL---D 375 SV + + T ++ F + E P + P ++ P R+K AL D Sbjct: 312 SVAA--SIATHLSAVIPNFYV-----QEHFPYWARIPGWIEVATEPFESRLKNGALQIPD 364 Query: 376 APGFGVRL 383 PG+GV L Sbjct: 365 GPGYGVTL 372 Lambda K H 0.321 0.140 0.444 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: 392 Number of extensions: 20 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 395 Length of database: 386 Length adjustment: 31 Effective length of query: 364 Effective length of database: 355 Effective search space: 129220 Effective search space used: 129220 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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