Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate Ga0059261_4216 Ga0059261_4216 Dihydroxyacid dehydratase/phosphogluconate dehydratase
Query= BRENDA::Q1PAG1 (608 letters) >FitnessBrowser__Korea:Ga0059261_4216 Length = 573 Score = 220 bits (561), Expect = 1e-61 Identities = 172/542 (31%), Positives = 265/542 (48%), Gaps = 38/542 (7%) Query: 32 SDGPQRGKLQCANFAHGVAGCGSEDKHSLRMMNAANVAIVSSYNDMLSAHQPYEHFPEQI 91 S GP+R + +A G+ SE++ + VA+ S+ ND + + + Sbjct: 16 SVGPERAPHRSYYYAMGI----SEEEIARPF-----VALASAGNDSAPCNTTLDAQADAA 66 Query: 92 KKALREMGSVGQFAGGTPAMCDGVTQGEAGMELSLPSREVIALSTAVALSHNMFDAALML 151 +K + + G + + T + DG+ G GM+ SL SREVIA S +++ + +DA + Sbjct: 67 RKGVADNGGLPR-RFNTITVTDGIAMGHQGMKSSLVSREVIADSVELSVRGHCYDALVGF 125 Query: 152 GICDKIVPGLMMGALRFGHLPTIFVPGGPMPSG------ISNKEKADVRQRYAEGKATRE 205 CDK +PG+MM LR ++P+IFV GG + G ++ + +V ++A G Sbjct: 126 AGCDKSLPGMMMAMLRL-NIPSIFVYGGSILPGRYQDRDVTVVDVFEVVGKFAAGTCPIS 184 Query: 206 ELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLHLPGASFVN-PYTPLRDALTHEAAQQ 264 E+ E + G C TANT + E +GL LP ++ V PYT R+ + A Q Sbjct: 185 EVHALEKVACPGHGACGGQYTANTMACVGEAIGLSLPNSNMVPAPYTS-REQIAVAAGYQ 243 Query: 265 VTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGSTNHTLHMPAIAQAAGIQLTWQDMA 324 V L ++ N P +I + +N+ + ATGGSTN LH+PA+A AGI D+A Sbjct: 244 VMELLER--NIRP-RDICTREAFINAARIVAATGGSTNGALHLPAMASEAGIDFDLFDVA 300 Query: 325 DLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIRELLEAGLLHEDVNTVAGRGLSRYTQE 384 ++ + P + + P GK AGG+ L++ +LE GLL+ D TV G+ L + Sbjct: 301 EVFKSTPYAADLKPGGKYVAKDMYEAGGVYMLMKSMLENGLLYGDCMTVTGKTLGENIDQ 360 Query: 385 PFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGLRVMEGNLGRGVMKVSAVALQHQIV 444 + W D+ ++ V +P GG+ + G L V + + Sbjct: 361 -------VTWNP------DQKVIYDVRTPITPTGGVVGLRGTLAPNGAIVKVAGMSRLVF 407 Query: 445 EAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPRSN-GMPELHKMTPFLGVLQDRGFK 503 E PA F ++D A + E+ + V V+R++GP+ GM E+ T L L G K Sbjct: 408 EGPARCFDCEEDAFAAVEKREIREGEVVVIRYEGPKGGPGMREMLSTTAALYGL-GMGEK 466 Query: 504 VALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRDGDIIRVDGVKGTLELKVDADEFA 563 VAL+TDGR SGA+ HV PEA G +A V DGD IR+D GT++L V D A Sbjct: 467 VALITDGRFSGATRGFCIG-HVGPEAAECGPIALVEDGDTIRIDAEAGTIDLHVAEDVLA 525 Query: 564 AR 565 R Sbjct: 526 ER 527 Lambda K H 0.318 0.134 0.386 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: 963 Number of extensions: 57 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: 608 Length of database: 573 Length adjustment: 37 Effective length of query: 571 Effective length of database: 536 Effective search space: 306056 Effective search space used: 306056 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