Align D-glucosaminate dehydratase (EC 4.3.1.9) (characterized)
to candidate N515DRAFT_2222 N515DRAFT_2222 D-serine dehydratase
Query= reanno::pseudo5_N2C3_1:AO356_00450 (405 letters) >FitnessBrowser__Dyella79:N515DRAFT_2222 Length = 426 Score = 371 bits (953), Expect = e-107 Identities = 197/396 (49%), Positives = 263/396 (66%), Gaps = 9/396 (2%) Query: 15 ATVGAHLLK-DVSLPALVLHRAALEHNIRWMQAFVTDSGAELAPHGKTSMTPALFRRQLD 73 A+ G +LLK D+SLP VL ++ LEHN+ WMQ F ++ GA LAPHGKT+M P LF RQL+ Sbjct: 35 ASHGWNLLKEDLSLPVAVLSQSRLEHNLAWMQRFASEYGARLAPHGKTTMAPRLFARQLE 94 Query: 74 AGAWGLTLATAVQTRAAYAHGVRRVLMANQLVGTPNMALIADLLADPAFEFHCMVDHPDN 133 AGAWG+TLATA Q RAAY HGVRR+L+ANQLVG NMA++A+LLADP+FEF C+VD + Sbjct: 95 AGAWGITLATAQQARAAYVHGVRRILLANQLVGRRNMAIVAELLADPSFEFFCLVDAAEQ 154 Query: 134 VADLGAFFASRGMKLNVMIEYGVVGGRCGCRTEAEVLALAEAI-RSQPALALTGIEGYEG 192 V L AFF + G ++ V+IE GV GGR G R EA+ A+ +A+ +S A++L G+E YEG Sbjct: 155 VRQLAAFFGAAGRRIQVLIELGVPGGRTGVRDEAQWQAVLDALAQSGGAVSLAGVEVYEG 214 Query: 193 VIHGDHAISGIRAFAASLVRLAVQLQDDDAFAIDKPIITASGSAWYDLIAESFEAQNAHG 252 V+ + A IRAF V L D +++ +GSAWYD++AE F Sbjct: 215 VLKDETA---IRAFLQRGVEAVQVLARDGRLQRTPAVLSGAGSAWYDVVAEEFAKAQIGA 271 Query: 253 RFLSVLRPGSYVAHDHGIYKEAQCCV---LERRSDLHEGLRPALEVWAHVQSLPEPGFAV 309 VLRPG Y+ HD G Y+ AQ + + + L PAL+VWA+VQS+PEP A+ Sbjct: 272 PLDVVLRPGCYLTHDVGAYRIAQARIDASNPQARRMRSSLLPALQVWAYVQSVPEPECAI 331 Query: 310 IALGKRDVAYDAGLPVPLKRYTPGSDSVPGDDVSGCKVTAVMDQHAFMSVAAGVELRVGD 369 +A+GKRD A+DAG P P + PG S P +VT +MDQHA++ +AAG +LRVGD Sbjct: 332 VAMGKRDAAFDAGFPSPAAHFRPGG-SAPSPVPPHWEVTGMMDQHAYLKIAAGDDLRVGD 390 Query: 370 IIAFGTSHPCLTFDKWRVGCLVDEQLRVVESMETCF 405 ++AF SHPCLTFDKWR ++D+ VV+ ++T F Sbjct: 391 MLAFDISHPCLTFDKWRQLPVIDDAYDVVDVVQTYF 426 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: 525 Number of extensions: 24 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: 426 Length adjustment: 31 Effective length of query: 374 Effective length of database: 395 Effective search space: 147730 Effective search space used: 147730 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