Align phosphogluconate dehydratase (characterized)
to candidate HSERO_RS22480 HSERO_RS22480 dihydroxy-acid dehydratase
Query= CharProtDB::CH_024239 (603 letters) >FitnessBrowser__HerbieS:HSERO_RS22480 Length = 594 Score = 174 bits (442), Expect = 7e-48 Identities = 142/454 (31%), Positives = 208/454 (45%), Gaps = 42/454 (9%) Query: 146 DGALFLGVCDKIVPGLTMAALSFGHLPAVFVPSGPMASGLPNKEKV-------RIRQLYA 198 D + CDK P MAA + +PA+ + GPM G + E V + R+L + Sbjct: 122 DAVVLTTGCDKTTPSQIMAAATVD-IPAIVLSGGPMLDGWMDGELVGSGSAIWKGRKLLS 180 Query: 199 EGKVDRMALLESEAASYHAPGTCTFYGTANTNQMVVEFMGMQLPGSSFVHPDSPLRDALT 258 G +D LE AAS + G C GTA+T + E +GM L G S + R + Sbjct: 181 AGSIDNEKFLEIAAASAPSSGHCNTMGTASTMNAMAEALGMSLTGCSAIPAPYRERGQMA 240 Query: 259 AAAARQVTRMTGNGNEWMPIGKMIDEKVVVNGIVALLATGGSTNHTMHLVAMARAAGIQI 318 R R+ G E + ++ ++ IV A GGSTN H++AMAR AG+++ Sbjct: 241 YETGR---RIVGMAYEDLRPSAILTRDAFLDAIVVNAAIGGSTNAQPHIMAMARHAGVEL 297 Query: 319 NWDDFSDLSDVVPLMARLYPNGPADINHFQAAGGVPVLVRELLKAGLLHEDVNTVAGFGL 378 +D+ VPL+ + P G F AGGVP ++ EL +AG L + T G + Sbjct: 298 QSEDWMKYGYDVPLLLNMQPAGKYLGERFHRAGGVPAIMWELQQAGKLRAERITATGKTM 357 Query: 379 SRYTLEPWLNNGELDWREGAEKSLDSNVIASFEQPFSHHGGTKVLSGNL-GRAVMKTSAV 437 + L R S D +I F P G VL GNL A+MKTS + Sbjct: 358 AE----------NLQGR----ASNDREMIYPFAAPLRERAGFLVLKGNLFDFAIMKTSVI 403 Query: 438 -----------PVENQVIEAPAVVFESQHDVMPAFE--AGLLDRDCVVVVRHQGPKA-NG 483 P + + E AVVF+ D A +D + ++ +R GP G Sbjct: 404 SETFRERYLSTPGQENIFECRAVVFDGSDDYHARINDPALKIDENTLLAIRGAGPVGWPG 463 Query: 484 MPELHKLMPPLGVLLDRCFKIALVTDGRLSGASGKVPSAIHVTPEAYDGGLLAKVRDGDI 543 E+ + PP ++ + + DGR SG S PS ++ +PE+ GG LA +RDGD Sbjct: 464 SAEVVNMQPPDALIKRGVSTLPTLGDGRQSGTSDS-PSILNASPESAVGGGLAYLRDGDR 522 Query: 544 IRVNGQTGELTLLVDEAELAAREPH-IPDLSASR 576 +R++ TGE +LV E ELA R+ IP + S+ Sbjct: 523 VRIDLNTGECNMLVSEEELARRKSEGIPPVPPSQ 556 Lambda K H 0.318 0.134 0.392 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: 816 Number of extensions: 40 Number of successful extensions: 3 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: 603 Length of database: 594 Length adjustment: 37 Effective length of query: 566 Effective length of database: 557 Effective search space: 315262 Effective search space used: 315262 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 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