Align D-glucosaminate dehydratase (EC 4.3.1.9) (characterized)
to candidate BWI76_RS03885 BWI76_RS03885 hypothetical protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2867 (405 letters) >FitnessBrowser__Koxy:BWI76_RS03885 Length = 404 Score = 328 bits (842), Expect = 1e-94 Identities = 189/408 (46%), Positives = 242/408 (59%), Gaps = 20/408 (4%) Query: 5 PNTAAVEKGTAPKGASLVRDVSLPALVLHREALEHNIRWMQAFVSDSGAELAPHGKTSMT 64 P+ AAV A L +V LPA +L + ALE+NI WMQ + G LAPHGKT+MT Sbjct: 10 PHKAAVMSAPANL---LAEEVCLPAALLKKTALENNIAWMQRYADARGVSLAPHGKTTMT 66 Query: 65 PALFRRQLDAGAWGITLASATQTRAAYAHGVRRVLMANQLVGTPNMALIADLLAD-PTFD 123 P +F+ Q AGAWGI SA Q AA A GV RVLM NQLVG NM ++ L A D Sbjct: 67 PWIFQAQQRAGAWGIGAGSAWQAGAAMASGVERVLMVNQLVGRANMQAVSRLKAHYRAAD 126 Query: 124 FYCMVDHPDNVADLGAYFASRGVRLNVMIEYGVVGGRCGCRSEQQVLDLAKAIAAQPALA 183 F C +D N L A+F+ R L+V+IE GV GGRCGCRS L LA+A+A P L Sbjct: 127 FICCIDSLANARALSAFFSERRQTLDVLIELGVAGGRCGCRSVDDALTLAQAVADLPGLK 186 Query: 184 LTGIEGYEGVIHGDHAVTGIRDFAASLVRLAVQLQD--SGAFAIPKPIITASGSAWYDLI 241 L G+E YEGV+HGD + LA +++ G F ++T +G+ WYD++ Sbjct: 187 LRGLELYEGVLHGDDPQPQVEVLLRQAADLACRMEHLVEGEF-----VLTGAGTVWYDVV 241 Query: 242 AESFEAQNAAGRFLSVLRPGSYVAHDHGIYKEAQCCVLDR---RSDLHEGLRPALEVWAH 298 + A R V+RPG Y+ HD GIY AQ ++ R DL L ALE+ A Sbjct: 242 CNIWLAAQKPARCRIVIRPGCYITHDRGIYDIAQKALVARDPIACDLGGDLTSALELMAM 301 Query: 299 VQSLPEPGFAVIALGKRDVAYDAGLPVPLLRYKAGV-VPAEGDDVSVCKVTAVMDQHAFM 357 VQS+PE AV+ GKRD A+DAGLP P+ RY+ G + AEG + +MDQH + Sbjct: 302 VQSVPEADRAVVNFGKRDCAFDAGLPQPIDRYRNGERLSAEG-----IESVGIMDQHCML 356 Query: 358 TVAPGVDLRVGDIISFGTSHPCLTFDKWRVGCLVDEQLNVIETMETCF 405 +APG D++VGDI+ FGTSHPCLTFDKW+ LVDEQ NV+E ++T F Sbjct: 357 RLAPGSDVQVGDILVFGTSHPCLTFDKWKTLLLVDEQYNVLEELDTLF 404 Lambda K H 0.322 0.136 0.413 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: 420 Number of extensions: 18 Number of successful extensions: 5 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: 405 Length of database: 404 Length adjustment: 31 Effective length of query: 374 Effective length of database: 373 Effective search space: 139502 Effective search space used: 139502 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