Align Phosphogluconate dehydratase; EC 4.2.1.12; 6-phosphogluconate dehydratase (uncharacterized)
to candidate RR42_RS31070 RR42_RS31070 dihydroxy-acid dehydratase
Query= curated2:P31961 (608 letters) >FitnessBrowser__Cup4G11:RR42_RS31070 Length = 576 Score = 191 bits (485), Expect = 7e-53 Identities = 159/486 (32%), Positives = 236/486 (48%), Gaps = 51/486 (10%) Query: 105 AGGVPAMCDGVTQGEP-GMELSLASRDVIAMSTAIALSHNMFDAALCLGVCDKIVPGLLI 163 AGG+P ++ E S+ R++++M T + DA + +G CDK VP L+ Sbjct: 75 AGGLPVDFPTISVHESFSAPTSMYLRNLMSMDTEEMIRAQPMDAVVLIGGCDKTVPAQLM 134 Query: 164 GSLRFGHLPTVFVPAGPMPTGISNKEKAAV----RQLFAEGKATREELLASEMASYH--- 216 G+ G +P + + G M TG E+ R+ + G+ EE+ A E+A + Sbjct: 135 GAASAG-VPAIQLVTGSMLTGSHRGERVGACTDCRRYW--GRYRAEEIDAPEIADVNNQL 191 Query: 217 --APGTCTFYGTANTNQLLVEVMGLHLPGASFVNPNTPLRDEL-----TREAARQASRLT 269 + GTC+ GTA+T L E +G+ + G + T R + T A S LT Sbjct: 192 VASVGTCSVMGTASTMACLTEALGMMVAGGASAPAVTADRVRVAERTGTTAVAMARSGLT 251 Query: 270 PENGNYVPMAEIVDEKAIVNSVVALLATGGSTNHTLHLLAIAQAAGIQLTWQDMSELSHV 329 PE I+ +AI N++ LLA GGSTN +HL AIA GI + + +S Sbjct: 252 PER--------ILTGRAIENAIRVLLAIGGSTNGIVHLTAIAGRLGIGIDLAGLDRMSRE 303 Query: 330 VPTLARIYPNGQADINHFQAAGGMSFLIRQLLDGGLLHEDVQTVAGPGLRRYTREPFLED 389 P L + P+GQ + F AAGGM L+R+L LLH D TV+G L Sbjct: 304 TPVLVDLKPSGQHYMEDFHAAGGMPALLRELRP--LLHLDTLTVSGRTLGEEL------- 354 Query: 390 GRLVWREGPERSLDEAILRPLDKPFSAEGGLRLMEGNL--GRGVMKVSAVAPEHQVVEAP 447 + + ++RP D P GGL ++ GNL G ++K SA P E Sbjct: 355 ------DAAPAPFAQEVIRPFDAPIYPVGGLAVLRGNLAPGGAIIKQSAADPVLMEHEGR 408 Query: 448 VRIFHDQASLAAAF--KAGELERDLVAVVRFQGPR-ANGMPELHKLTPFLGVLQDRGFK- 503 +F D +A A +++ D + V++ GP A GMPE + P L G K Sbjct: 409 AVVFEDAEDMALRIDDDALDVKADDILVLKRIGPTGAPGMPEAGYM-PIPRKLARAGVKD 467 Query: 504 VALVTDGRMSG-ASGKVPAAIHVSPEAIAGGPLARLRDGDRVRVDGVNGELRVLVDDAEW 562 + ++DGRMSG A+G + +HV+PEA GGPLA +R+GDR+R+ E+ +L+DDAE Sbjct: 468 MVRISDGRMSGTAAGTI--VLHVTPEAAIGGPLAHVRNGDRIRLSVARREISLLIDDAEL 525 Query: 563 QARSLE 568 R+ E Sbjct: 526 ARRAAE 531 Lambda K H 0.319 0.135 0.397 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: 807 Number of extensions: 43 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: 608 Length of database: 576 Length adjustment: 37 Effective length of query: 571 Effective length of database: 539 Effective search space: 307769 Effective search space used: 307769 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: 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