Align D-glucosaminate dehydratase (EC 4.3.1.9) (characterized)
to candidate RR42_RS28855 RR42_RS28855 amino acid deaminase
Query= reanno::pseudo3_N2E3:AO353_21740 (405 letters) >FitnessBrowser__Cup4G11:RR42_RS28855 Length = 422 Score = 370 bits (951), Expect = e-107 Identities = 197/397 (49%), Positives = 262/397 (65%), Gaps = 9/397 (2%) Query: 14 AGQPGANLV-RDVSLPALVLHREALEHNIHWMQAFVSHSGAELAPHGKTSMTPSLFRRQL 72 AGQ G L+ D+SLPA VL+ E L HN+ WM+ F+ G +LAPHGKT+M P LF RQL Sbjct: 30 AGQVGWQLLAEDLSLPAAVLYEERLAHNLEWMRRFMGEYGVQLAPHGKTTMAPKLFARQL 89 Query: 73 EAGAWGITLATVVQTRAAYAHGVRRVLMANQLVGAPNMALIAELLADPSFDFYCMVDHPD 132 AGAWGITLAT QT AAYAHGVRRVLMANQLVG NM ++A+LL DP F+F+ +VD Sbjct: 90 AAGAWGITLATAHQTAAAYAHGVRRVLMANQLVGRRNMEIVADLLRDPDFEFFTLVDSAA 149 Query: 133 NVADLGVFFAARGLRLNVMIEYGVVGGRCGCRSEAEVLALAEAIKAQPG-LALTGIEGYE 191 V LG +F+ARG +L V++E GV GGR G R + A+ A+ PG L+L G+E YE Sbjct: 150 LVDQLGRYFSARGQKLQVLLELGVPGGRTGVRGAQQQAAVLAALARWPGVLSLAGVEIYE 209 Query: 192 GVIHGDQAVSGIREFAASLVRLAVQLQDSGAFAISKPIITASGSAWYDLIAESFEAQNAG 251 GV+ Q + IR+F V + +L +G F S +++ +GSAWYD++AE F + G Sbjct: 210 GVL---QEEADIRDFLRRTVAVTRELFAAGRFGRSPVVMSGAGSAWYDVVAEEFARTDIG 266 Query: 252 GRFLSVLRPGSYVAHDHGIYKEAQCCVLDRR---SDLHEGLRPALEVWAHVQSLPEPGFA 308 VLRPG Y+ HD GIY+ AQ +L + EGL PAL++WA+VQS+PEP A Sbjct: 267 APIDIVLRPGCYLTHDVGIYRAAQKRILASNPVAQKMREGLLPALQLWAYVQSIPEPERA 326 Query: 309 VIALGKRDVAYDAGLPVPLLRYRAGVLPAVGDDVSACTVTAVMDQHAFMTVAPGVQLRVG 368 +I +GKRD A+DAG+P+P YR G V + VT +MDQHA++ + PG ++VG Sbjct: 327 IIGMGKRDAAFDAGMPIPAQVYRPGASVPVAVP-AHWEVTGMMDQHAYLAIRPGDDVQVG 385 Query: 369 DIISFGTSHPCLTFDKWRTGCLVDEQLNVIESMETCF 405 D+++F SHPCLTFDKWR ++D L VI+ ++T F Sbjct: 386 DMVAFDISHPCLTFDKWRHIPVLDGDLRVIDLVQTFF 422 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: 505 Number of extensions: 26 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: 422 Length adjustment: 31 Effective length of query: 374 Effective length of database: 391 Effective search space: 146234 Effective search space used: 146234 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