Align L-talarate dehydratase (EC 4.2.1.156); galactarate dehydratase (EC 4.2.1.42) (characterized)
to candidate H281DRAFT_06497 H281DRAFT_06497 L-alanine-DL-glutamate epimerase
Query= BRENDA::Q8ZL58 (398 letters) >FitnessBrowser__Burk376:H281DRAFT_06497 Length = 374 Score = 172 bits (435), Expect = 2e-47 Identities = 115/343 (33%), Positives = 186/343 (54%), Gaps = 17/343 (4%) Query: 64 IAEIRSRDGFEGVGFSYSKRAGGQGIYAHAKE--IADNLLGEDPNDIDKIYTKLLWAGAS 121 + ++RS DG EG+GF Y A G+ I+ A E +A L G D +++ ++ ++ Sbjct: 34 LVKVRSSDGAEGIGFCYVGNAAGE-IFRVAVEQLLAPVLNGRDSLEVEGLWKEMYQESLL 92 Query: 122 VGRSGMAVQAISPIDIALWDMKAKRAGLPLAKLLGA-HRDSVQCYNTSGGFLH-TPLDQV 179 GR G ++A+S +DIALWD+ A+ AGLPL K LGA D V Y + G ++ ++V Sbjct: 93 QGRMGTVMRALSALDIALWDLNARTAGLPLHKYLGAVELDHVDAYASGGYYVDGKTAEEV 152 Query: 180 LKNVVISRENGIGGIKLKVGQPNCAEDIRRLTAVREALGDEFPLMVDANQQW-DRETAIR 238 + + G +K+K G+ + A + R+ A REA+G + LM+D N W D A++ Sbjct: 153 GEEMASYVALGFKAVKMKTGRWSPAGEESRVKAAREAIGPDVELMLDCNNGWVDTVQAMQ 212 Query: 239 MGRKMEQFNLIWIEEPLDAYDIEGHAQLAAALDTPIATGEMLTSFREHEQLILGNASDFV 298 R+ EQ++ +IEEP DIE HA+LA P+AT E+ H+QL+ + + Sbjct: 213 YLRRFEQYDPYFIEEPFSPDDIESHARLAKLTRIPVATAEIGYGRWYHKQLLDMGGASIL 272 Query: 299 QPDAPRVGGISPFLKIMDLAAKHGRKLAPHFAMEVHLHLSAAYPLEPWLEHFEWLNPLFN 358 Q DA GGI+ + +I +A+ +G ++ PH+ +VH L AA ++E F W + + N Sbjct: 273 QTDAAVCGGITEWRRIAAMASGYGIQMCPHWFHDVHAPLVAATQNARYVEFF-WDDQVLN 331 Query: 359 ------EQLELRDGRMWISDRHGLGFTLSE----QARRWTQLT 391 QL ++GR+ + GLGF E + RWT+++ Sbjct: 332 FRRLVDRQLTHKEGRVLLHQTPGLGFNFDEAEVARYGRWTKVS 374 Lambda K H 0.319 0.136 0.410 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: 377 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: 398 Length of database: 374 Length adjustment: 30 Effective length of query: 368 Effective length of database: 344 Effective search space: 126592 Effective search space used: 126592 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 (21.8 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