Align D-mannonate dehydratase; ManD; EC 4.2.1.8 (characterized)
to candidate AO356_28550 AO356_28550 bifunctional D-altronate/D-mannonate dehydratase
Query= SwissProt::A5V6Z0 (402 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28550 Length = 403 Score = 644 bits (1662), Expect = 0.0 Identities = 303/403 (75%), Positives = 346/403 (85%), Gaps = 1/403 (0%) Query: 1 MKITGARVIVTCPDRNFVTLKIETDEGLTGIGDATLNGRELAVASYLTDHVIPCLIGRDA 60 MKI ARVIVTCP RN VTLKI TDEGL GIGDATLNGRELAV +YL +HV+P LIGRDA Sbjct: 1 MKIVEARVIVTCPGRNLVTLKIVTDEGLYGIGDATLNGRELAVVAYLEEHVLPALIGRDA 60 Query: 61 HRIEDIWNYLYRGAYWRRGPVTMSAIAAVDTALWDIKAKAAGLPLYQLLGGRSRDGVMVY 120 HRIEDIW YLYRGAYWRRGPVTM+AIAAVD ALWDIKAKAA +PLYQLLGG+SR+ VMVY Sbjct: 61 HRIEDIWQYLYRGAYWRRGPVTMTAIAAVDVALWDIKAKAANMPLYQLLGGKSRERVMVY 120 Query: 121 GHANGRDIEETTDEVARYIEMGYRAIRAQTGVPGLASTYGVSSDK-MYYEPADAALPTEN 179 GHA G+DIE DEVAR++E+GY+A+R Q GVPG+A+TYGV+ YEPAD+ LP E+ Sbjct: 121 GHATGKDIEGCLDEVARHVELGYKAVRVQCGVPGIATTYGVAKRSGERYEPADSDLPAEH 180 Query: 180 IWSTEKYLDHVPKLFDRLRDRFGFDHHLLHDVHHRLTPIEAGRLGKSLEPYRLFWMEDAT 239 +W T KYL++VPKLF +R+RFG D H+LHDVHHRLTPIEAGRLGK++EPY LFW+ED T Sbjct: 181 VWDTAKYLNYVPKLFAAVRERFGDDLHILHDVHHRLTPIEAGRLGKAVEPYNLFWLEDCT 240 Query: 240 PAENQEAFRLIRQHTVTPLAVGEVFNTIWDAKDLIQNQLIDYIRATVVHAGGISHLRRIA 299 PAENQ++FRLIRQHT TPLAVGEVFN+I D ++LIQ QLIDYIR T+VHAGGI+H+RRIA Sbjct: 241 PAENQQSFRLIRQHTTTPLAVGEVFNSIHDCRELIQEQLIDYIRTTLVHAGGITHVRRIA 300 Query: 300 DLAALYQVRTGCHGATDLSPVCMGAALHFDIWVPNFGVQEYMRHTEATDAVFPHAYSFAS 359 D AAL+QVRTG HGATDLSPVCMGAALHFD WVPNFG+QE+M H + D VFPHAY F Sbjct: 301 DFAALFQVRTGFHGATDLSPVCMGAALHFDTWVPNFGIQEHMPHEDRIDEVFPHAYRFED 360 Query: 360 GYMTPGDVPGHGVEIDEKLAAKYPYKPCSLPVNRLEDGTLWHW 402 G+ TPG+ PGHGV+IDE LA +YPYK SLPVNRLEDGTLWHW Sbjct: 361 GHFTPGETPGHGVDIDEDLARQYPYKRASLPVNRLEDGTLWHW 403 Lambda K H 0.322 0.138 0.439 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: 666 Number of extensions: 33 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: 402 Length of database: 403 Length adjustment: 31 Effective length of query: 371 Effective length of database: 372 Effective search space: 138012 Effective search space used: 138012 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 (21.9 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