Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_152617477.1 BS73_RS01920 dihydroxy-acid dehydratase
Query= SwissProt::P9WKJ5 (575 letters) >NCBI__GCF_000744815.1:WP_152617477.1 Length = 572 Score = 327 bits (838), Expect = 8e-94 Identities = 221/562 (39%), Positives = 297/562 (52%), Gaps = 27/562 (4%) Query: 31 AAARGMLRAVGMDDEDFAKPQIGVASSWNEITPCNLSLDRLANAVKEGVFSAGGYPLEFG 90 A R RA+G+ DED KP+I V ++ +E+ C LD +A VKEGV +AGG P E Sbjct: 14 ATRRSQWRALGLSDEDMLKPKIAVVNTSSELAVCFSHLDGVAARVKEGVRAAGGLPFEVR 73 Query: 91 TISVSDGISMGHEGMHFSLVSREVIADSVEVVMQAERLDGSVLLAGCDKSLPGMLMAAAR 150 T + SD I G + L +R++I + +EV ++ +LDG + LA CDK+ PG LMAA R Sbjct: 74 TTAPSDFIHSAGHGGGYILSARDLIVNDIEVGVEGAQLDGMICLASCDKTAPGQLMAAGR 133 Query: 151 LDLAAVFLYAGSILPGRAKLSDGSERDVTIIDAFEAVGACSRGLMSRADVDAIERAICPG 210 LD+ + L G P + + + + + A GA ++ DA+ G Sbjct: 134 LDIPTLLLACG-YQPSGSYRGEHCDIEDVFLHACGTPGAELTAELTEMSEDAVR-----G 187 Query: 211 EGACGGMYTANTMASAAEALGMSLPGSAAPPATDRRRDGFARRSGQAVVELLRRGITARD 270 G C GM TAN+M AEALGM+LPGS A A R+ +VEL+R + R Sbjct: 188 PGVCAGMGTANSMHIVAEALGMALPGSTPVAADSPAMWREADRAAARIVELVREDVRPRA 247 Query: 271 ILTKEAFENAIAVVMAFGGSTNAVLHLLAIAHEANVALS-LQDFSRIGSGVPHLADVKPF 329 +LT AF NA+ V ++ G S N V HL A+A EA V L L F+ G+ P L+ V+P Sbjct: 248 VLTAAAFRNAVRVALSVGASINTVKHLQAVAAEAEVDLDVLGLFAEYGAVTPLLSAVRPN 307 Query: 330 GRHVMSDVDHIGGVPVVMK--ALLDAGLLHGDCLTVTGHTMAENLAAITPPDP------- 380 G H + D GG VM+ A LD GLL D TV+GH + ENLA DP Sbjct: 308 GPHTIEQFDAAGGARAVMRRLAALD-GLLDLDAPTVSGHIVGENLAGAEATDPATDRDTD 366 Query: 381 -----DGKVLRALANPIHPSGGITILHGSLAPEGAVVKTAGFDSD---VFEGTARVFDGE 432 +V+R P I IL GSL P G +VK + D + F G AR F+ + Sbjct: 367 TEADAHAEVIRPADRPFSREPLIVILRGSLCPLGGIVKLS-VDHERPTGFSGPARCFERQ 425 Query: 433 RAALDALEDGTITVGDAVVIRYEGPKGGPGMREMLAITGAIKGAGLGKDVLLLTDGRFSG 492 A+ AL G I GD VV+R GP+G PGM I A+ AGL V ++TDG+ SG Sbjct: 426 EDAVAALAAGAIGAGDVVVLRGLGPRGRPGMGMASQIVFALDRAGLTGRVAVVTDGQLSG 485 Query: 493 -GTTGLCVGHIAPEAVDGGPIALLRNGDRIRLDVAGRVLDVLADPAEFASRQQDFSPPPP 551 G+ VG + PEA DGGP+AL+R+GDRIR+DV GR ++ +PAE R+ + P Sbjct: 486 LVNRGIVVGEVRPEAADGGPLALVRDGDRIRVDVPGRGCELDVEPAELERRRAERPTLPE 545 Query: 552 RYTTGVLSKYVKLVSSAAVGAV 573 G LS Y + V A GAV Sbjct: 546 YGERGWLSVYRRTVQPLADGAV 567 Lambda K H 0.318 0.136 0.393 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: 978 Number of extensions: 59 Number of successful extensions: 7 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: 575 Length of database: 572 Length adjustment: 36 Effective length of query: 539 Effective length of database: 536 Effective search space: 288904 Effective search space used: 288904 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.
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