Align D-glucosaminate dehydratase (EC 4.3.1.9) (characterized)
to candidate BPHYT_RS03115 BPHYT_RS03115 amino acid deaminase
Query= reanno::pseudo5_N2C3_1:AO356_00450 (405 letters) >FitnessBrowser__BFirm:BPHYT_RS03115 Length = 425 Score = 380 bits (977), Expect = e-110 Identities = 199/391 (50%), Positives = 264/391 (67%), Gaps = 10/391 (2%) Query: 21 LLKDVSLPALVLHRAALEHNIRWMQAFVTDSGAELAPHGKTSMTPALFRRQLDAGAWGLT 80 L +DVSLPA VL+ +EHN++WMQAFV G +LAPHGKT+M P LFRRQL+ GAWG+T Sbjct: 39 LNEDVSLPAAVLYADRVEHNLKWMQAFVAQYGVKLAPHGKTTMAPQLFRRQLENGAWGIT 98 Query: 81 LATAVQTRAAYAHGVRRVLMANQLVGTPNMALIADLLADPAFEFHCMVDHPDNVADLGAF 140 LATA Q RAAY GV R+LMANQLVG NM ++A+LL+DP FEF C+VD + V LG F Sbjct: 99 LATAHQVRAAYHGGVSRILMANQLVGRHNMMMVAELLSDPDFEFFCLVDSVEGVEQLGEF 158 Query: 141 FASRGMKLNVMIEYGVVGGRCGCRTEAEVLALAEAIRSQP-ALALTGIEGYEGVIHGDHA 199 F S +L V++E GV GGR G R A+ A+ +AI P L L G+E YEGV+ +H Sbjct: 159 FKSVNKQLQVLLELGVPGGRTGVRDAAQRNAVLDAIARYPDTLKLAGVELYEGVLKEEHE 218 Query: 200 ISGIRAFAASLVRLAVQLQDDDAFAIDKPIITASGSAWYDLIAESFEAQNAHGRFLSVLR 259 +R F S V + +L + FA +++ +GSAWYD++AE F + G+ VLR Sbjct: 219 ---VREFLQSAVAVTRELVEQGRFARTPAVLSGAGSAWYDVVAEEFVKASETGKVEVVLR 275 Query: 260 PGSYVAHDHGIYKEAQCCVLERR---SDLHEGLRPALEVWAHVQSLPEPGFAVIALGKRD 316 PG Y+ HD GIY++AQ + R + EGL PAL++WA+VQS+PEP A+I LGKRD Sbjct: 276 PGCYLTHDVGIYRKAQTDIFARNPVARKMGEGLLPALQLWAYVQSIPEPDRAIIGLGKRD 335 Query: 317 VAYDAGLPVPLKRYTPGSDSVPGDDVS--GCKVTAVMDQHAFMSVAAGVELRVGDIIAFG 374 A+DAG+P P + Y PG+++ P D + G ++ +MDQHA++ + AG +L+VGD+IAF Sbjct: 336 SAFDAGMPEPARHYRPGNEA-PRDIAAGEGWEIFGLMDQHAYLRIPAGADLKVGDMIAFD 394 Query: 375 TSHPCLTFDKWRVGCLVDEQLRVVESMETCF 405 SHPCLTFDKWR +VD RV E +ET F Sbjct: 395 ISHPCLTFDKWRQVLVVDPAYRVTEVIETFF 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: 465 Number of extensions: 21 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