Align D-glucosaminate dehydratase (EC 4.3.1.9) (characterized)
to candidate H281DRAFT_01893 H281DRAFT_01893 D-serine dehydratase
Query= reanno::pseudo5_N2C3_1:AO356_00450 (405 letters) >FitnessBrowser__Burk376:H281DRAFT_01893 Length = 425 Score = 387 bits (995), Expect = e-112 Identities = 210/410 (51%), Positives = 274/410 (66%), Gaps = 12/410 (2%) Query: 4 VIPNAGVE-KGAATVGAHLL-KDVSLPALVLHRAALEHNIRWMQAFVTDSGAELAPHGKT 61 ++P A ++ AA + +LL +DVSLPA VL+ +EHN+ WMQAFV + G +LAPHGKT Sbjct: 20 MVPGASIQLTDAARLEWNLLNEDVSLPAAVLYADRVEHNLNWMQAFVAEYGVKLAPHGKT 79 Query: 62 SMTPALFRRQLDAGAWGLTLATAVQTRAAYAHGVRRVLMANQLVGTPNMALIADLLADPA 121 +M P LFRRQL+ GAWG+TLATA Q RAAY GV RVLMANQLVG NM ++A+LL+DP Sbjct: 80 TMAPQLFRRQLETGAWGITLATAHQVRAAYHGGVSRVLMANQLVGRRNMMMVAELLSDPD 139 Query: 122 FEFHCMVDHPDNVADLGAFFASRGMKLNVMIEYGVVGGRCGCRTEAEVLALAEAIRSQP- 180 FEF C+VD D V LG FF S L V++E GVVGGR G R EA+ A+ EAI P Sbjct: 140 FEFFCLVDSVDGVEQLGQFFTSVKKPLQVLLELGVVGGRTGVRDEAQRNAVLEAIARYPD 199 Query: 181 ALALTGIEGYEGVIHGDHAISGIRAFAASLVRLAVQLQDDDAFAIDKPIITASGSAWYDL 240 L L G+E YEGV+ +H +R F S V + L D+ F I++ +GSAWYD+ Sbjct: 200 VLKLAGVELYEGVLKEEHE---VREFLQSAVAVTRALLDEGRFDRTPAILSGAGSAWYDV 256 Query: 241 IAESFEAQNAHGRFLSVLRPGSYVAHDHGIYKEAQCCVLERR---SDLHEGLRPALEVWA 297 +AE F + G+ VLRPG Y+ HD GIY++AQ + R + EGL PAL++WA Sbjct: 257 VAEEFVKASETGKVEVVLRPGCYLTHDVGIYRKAQTDIFARNPVAKKMGEGLLPALQLWA 316 Query: 298 HVQSLPEPGFAVIALGKRDVAYDAGLPVPLKRYTPGSDSVPGDDVS--GCKVTAVMDQHA 355 +VQS+PEP A+I LGKRD A+DAGLP P + Y PG+ + P D + G +V +MDQHA Sbjct: 317 YVQSIPEPDRAIIGLGKRDSAFDAGLPEPARHYRPGNPA-PRDIAASEGWEVFGLMDQHA 375 Query: 356 FMSVAAGVELRVGDIIAFGTSHPCLTFDKWRVGCLVDEQLRVVESMETCF 405 ++ + AG +++VGD+IAF SHPCLTFDKWR ++D RV E +ET F Sbjct: 376 YLRIPAGADVKVGDMIAFDISHPCLTFDKWRQVLVLDSAYRVTEVIETFF 425 Lambda K H 0.322 0.136 0.414 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: 474 Number of extensions: 20 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: 425 Length adjustment: 31 Effective length of query: 374 Effective length of database: 394 Effective search space: 147356 Effective search space used: 147356 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