Align Phosphogluconate dehydratase; 6-phosphogluconate dehydratase; EC 4.2.1.12 (characterized)
to candidate BPHYT_RS25650 BPHYT_RS25650 dihydroxy-acid dehydratase
Query= SwissProt::P21909 (607 letters) >FitnessBrowser__BFirm:BPHYT_RS25650 Length = 588 Score = 197 bits (501), Expect = 1e-54 Identities = 162/495 (32%), Positives = 236/495 (47%), Gaps = 44/495 (8%) Query: 101 GATVQVAGGVPAMCDGVTQGQPGMEESLFSRDVIALATSVSLSHGMFEGAALLGI--CDK 158 G V + G ++ DG + GM SL SR+V+A SV L AL+G+ CDK Sbjct: 70 GGGVPIRGSAISVSDGTSMNHSGMRMSLVSREVVA--DSVELFVRAHNYDALIGVAGCDK 127 Query: 159 IVPGLLMGALRFGHLPTILVPSGPMTTGIP------------NKEKIRIRQLYA-----Q 201 +PG+LMG +R ++P + + G M G+ ++ + + A + Sbjct: 128 TLPGILMGMVRV-NVPGVFLFGGAMLPGVAPGQLPGGAGTGLQRQSTILTTIEAVGTTQR 186 Query: 202 GKIGQKELLDMEAACYHAEGTCTFYGTANTNQMVMEVLGLHMPGSAFVTPGTPLRQALTR 261 G + + +L +E C G+C TANT MV E LGL GSA V R A+ R Sbjct: 187 GDMSRAQLDAIEKQCTPTAGSCPGQFTANTMAMVAETLGLAPLGSAMVPAVYSERIAIAR 246 Query: 262 AAVHRVAELGWKGDDYRPLGK-IIDEKSIVNAIVGLLATGGSTNHTMHIPAIARAAGVIV 320 A V + +G PL + ++ +S+ NA + ATGGSTN +HIPAIA AG+ Sbjct: 247 RAGETVMRILTQGG---PLPRDLVTMESLENACAAVAATGGSTNAALHIPAIANEAGIRF 303 Query: 321 NWNDFHDLSEVVPLIARIYPNGPRDINEFQNAGGMAYVIKELLSANLLNRDVTTIAKGGI 380 +D + +PLI + P G + +AGG+ V+ LL+ L+ DV G + Sbjct: 304 ALDDVQRVFAKIPLIGDLQPGGRYLAQDLHHAGGVPAVLNALLAGGFLHGDVPAFGGGTL 363 Query: 381 EEYAKAPALNDAGELVWKPAGEPGDDTILRPVSNPFAKDGGLRLLEGNLGRAMYKASAVD 440 E AL+ A D ++RP P ++GGL +L GNL Sbjct: 364 AE-----ALS---------AFSGPDGIVVRPCDEPLGENGGLVILRGNLAPDGACLKIAG 409 Query: 441 PKFWTIEAPVRVFSDQDDVQKAFKAGELNKDVIVVVRFQGPRAN-GMPELHKLTPALGVL 499 K + VRVF ++D A + + ++V+R +GP+ GM E+ +T A+ Sbjct: 410 LKSLSFTGAVRVFECEEDCMAVVAARDYREGDVLVIRNEGPKGGPGMREMLGVTAAI-YG 468 Query: 500 QDNGYKVALVTDGRMSGATGKVPVALHVSPEALGGGAIGKLRDGDIVRISVEEGKLEALV 559 Q G KVAL+TDGR SGAT + + +V PEA GG IG LR+ D V I G L + Sbjct: 469 QGMGEKVALLTDGRFSGATRGMCIG-YVGPEAAAGGPIGLLRNDDRVHIDARAGILRVDL 527 Query: 560 PADEWNARPHAEKPA 574 DE AR A+ PA Sbjct: 528 SDDEL-ARRRADAPA 541 Lambda K H 0.318 0.136 0.403 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: 1047 Number of extensions: 62 Number of successful extensions: 6 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: 607 Length of database: 588 Length adjustment: 37 Effective length of query: 570 Effective length of database: 551 Effective search space: 314070 Effective search space used: 314070 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