Align D-mannonate dehydratase; ManD; EC 4.2.1.8 (characterized)
to candidate RR42_RS34970 RR42_RS34970 bifunctional D-altronate/D-mannonate dehydratase
Query= SwissProt::A5V6Z0 (402 letters) >FitnessBrowser__Cup4G11:RR42_RS34970 Length = 403 Score = 696 bits (1797), Expect = 0.0 Identities = 329/403 (81%), Positives = 364/403 (90%), Gaps = 1/403 (0%) Query: 1 MKITGARVIVTCPDRNFVTLKIETDEGLTGIGDATLNGRELAVASYLTDHVIPCLIGRDA 60 MKIT ARVIV P RNFVTLKIETDEGL+GIGDATLNGRELAVASYL DHV PCLIGRD Sbjct: 1 MKITAARVIVCSPGRNFVTLKIETDEGLSGIGDATLNGRELAVASYLEDHVAPCLIGRDP 60 Query: 61 HRIEDIWNYLYRGAYWRRGPVTMSAIAAVDTALWDIKAKAAGLPLYQLLGGRSRDGVMVY 120 H++EDIW YLYRGAYWRRGPVTMSAIAAVDTALWDIKAKAAG+PLYQLLGG+SR GVMVY Sbjct: 61 HQVEDIWQYLYRGAYWRRGPVTMSAIAAVDTALWDIKAKAAGMPLYQLLGGKSRTGVMVY 120 Query: 121 GHANGRDIEETTDEVARYIEMGYRAIRAQTGVPGLASTYGVSSDKMYYEPADAALPTENI 180 GHANG DIE T DEV RY E+GYRA+RAQ+GVPGL YGVSSD+++YEPADA+LP+E+ Sbjct: 121 GHANGSDIEATVDEVLRYKELGYRAVRAQSGVPGLNKVYGVSSDRLFYEPADASLPSEHD 180 Query: 181 WSTEKYLDHVPKLFDRLRDRFGFDHHLLHDVHHRLTPIEAGRLGKSLEPYRLFWMEDATP 240 WSTE+YLDH P+LF+++RD G+D HLLHDVHHRLTPIEA RLGKSLEP+RLFWMEDATP Sbjct: 181 WSTERYLDHTPRLFEKVRDAAGWDLHLLHDVHHRLTPIEAARLGKSLEPFRLFWMEDATP 240 Query: 241 AENQEAFRLIRQHTVTPLAVGEVFNTIWDAKDLIQNQLIDYIRATVVHAGGISHLRRIAD 300 AE+QE+FRLIRQHT TPLAVGEVFNTIWD K LIQ QLIDYIRATVVHAGGI+HLRRIAD Sbjct: 241 AEHQESFRLIRQHTTTPLAVGEVFNTIWDCKTLIQEQLIDYIRATVVHAGGITHLRRIAD 300 Query: 301 LAALYQVRTGCHGATDLSPVCMGAALHFDIWVPNFGVQEYMRHTEATDAVFPHAYSFASG 360 AA++QVRTG HGATDLSPVCMGAALHFD+WVPNFG+QEYMRH+E TDAVFPHAY+FA+G Sbjct: 301 FAAMHQVRTGSHGATDLSPVCMGAALHFDLWVPNFGIQEYMRHSEQTDAVFPHAYTFANG 360 Query: 361 YMTPGDVPGHGVEIDEKLAAKYPYKPCSLPVNRL-EDGTLWHW 402 + PGD PGHGV+IDE LAA+YPY+ LPVNRL DGTLWHW Sbjct: 361 MLYPGDAPGHGVDIDETLAARYPYQRAYLPVNRLAHDGTLWHW 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: 690 Number of extensions: 28 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: 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