Align Phosphogluconate dehydratase; 6-phosphogluconate dehydratase; EC 4.2.1.12 (characterized)
to candidate WP_011384917.1 AMB_RS12770 dihydroxy-acid dehydratase
Query= SwissProt::P21909 (607 letters) >NCBI__GCF_000009985.1:WP_011384917.1 Length = 616 Score = 211 bits (536), Expect = 1e-58 Identities = 178/588 (30%), Positives = 266/588 (45%), Gaps = 62/588 (10%) Query: 64 DFNRMNIGVVTSYNDMLSAHEPYYRYPEQMKVFAREVGATVQVAGGVP------AMCDGV 117 DF + I + S+ + H +K + V ++ AGGV A+ DG+ Sbjct: 31 DFGKPIIAIANSFTQFVPGHV-------HLKDLGQMVAREIEKAGGVAKEFDTIAIDDGI 83 Query: 118 TQGQPGMEESLFSRDVIALATSVSLSHGMFEGAALLGICDKIVPGLLMGALRFGHLPTIL 177 G GM SL SR++IA + ++ + + CDKI PG+LM +LR ++PTI Sbjct: 84 AMGHAGMLYSLPSRELIADSVEYMVNAHCADAMVCISNCDKITPGMLMASLRL-NIPTIF 142 Query: 178 VPSGPMTTG--IPNKEKIRIRQLYAQGKIGQKELLDMEAACYHAE-----GTCTFYGTAN 230 + GPM G E + + A K + + D EA + E G+C+ TAN Sbjct: 143 ISGGPMEAGKVTYQGETHAVDLIDAMIKGADQNVSDEEALAFEKESCPTCGSCSGMFTAN 202 Query: 231 TNQMVMEVLGLHMPGSAFVTPGTPLRQALTRAAVHRVAELG---WKGDDYRPLGKIIDE- 286 + ++E LGL +PG+ V R+ L A R+ +L ++GDD L + I Sbjct: 203 SMNCLIEALGLGLPGNGTVVATHADRKELFLEAGRRIVDLARRAYEGDDASVLPRSIATF 262 Query: 287 KSIVNAIVGLLATGGSTNHTMHIPAIARAAGVIVNWNDFHDLSEVVPLIARIYPNGPR-D 345 ++ NA+ +A GGSTN +H+ A A+ AGV +D LS VP + ++ PN P Sbjct: 263 QAFENAMTLDIAMGGSTNTVLHLLAAAQEAGVAFGMSDIDRLSRRVPCLCKVAPNVPDVH 322 Query: 346 INEFQNAGGMAYVIKELLSANLLNRD-----VTTIAKG-------------GIEEYAKAP 387 I + AGG+ ++ +L L+NR+ T+A+G +E Y AP Sbjct: 323 IEDVHRAGGIMGILGQLDRGGLINRECGTIHARTLAEGLDRWDISRSNDPKVVEFYKAAP 382 Query: 388 ALNDAGELV-----WKPAGEPGDDTILRPVSNPFAKDGGLRLLEGNLG--RAMYKASAVD 440 E W + ++R V N F+KDGGL +L GNL + K + VD Sbjct: 383 GGVRTTEAFSQSKRWAEVDKDRTAGVIRSVDNAFSKDGGLAVLFGNLALDGCIVKTAGVD 442 Query: 441 PKFWTIEAPVRVFSDQDDVQKAFKAGELNKDVIVVVRFQGPRAN-GMPELHKLTPALGVL 499 K T P + QD+ G++ +V+VR++GPR GM E+ T L + Sbjct: 443 DKNLTFSGPAVICESQDEAVAKILGGQVKSGDVVIVRYEGPRGGPGMQEMLYPTSYLKSM 502 Query: 500 QDNGYKVALVTDGRMSGATGKVPVALHVSPEALGGGAIGKLRDGDIVRISVEEGKLEALV 559 G + AL+TDGR SG T + + HVSPEA GGAIG ++ GDI+ I + + V Sbjct: 503 -GLGKECALITDGRFSGGTSGLSIG-HVSPEAAEGGAIGLIQAGDIIDIHIPNRSIAIRV 560 Query: 560 PADEWNAR--------PHAEKPAFRPGTGRELFDIFRQNAAKAEDGAV 599 E R P A KP R + A GAV Sbjct: 561 SDAELEKRRQAMQALGPKAWKPVDRDRQVSAALRAYAAMTTSAARGAV 608 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: 988 Number of extensions: 53 Number of successful extensions: 9 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: 616 Length adjustment: 37 Effective length of query: 570 Effective length of database: 579 Effective search space: 330030 Effective search space used: 330030 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