Align Phosphogluconate dehydratase; EC 4.2.1.12 (uncharacterized)
to candidate WP_039951110.1 BUB52_RS01630 dihydroxy-acid dehydratase
Query= curated2:P56111 (608 letters) >NCBI__GCF_900129655.1:WP_039951110.1 Length = 600 Score = 207 bits (528), Expect = 8e-58 Identities = 162/529 (30%), Positives = 261/529 (49%), Gaps = 42/529 (7%) Query: 69 AIITAYNDMLSAHQPFKNYPDLIKKELQEHNAYASVASGVPAMCDGITQGYDGMELSLFS 128 AI+ ++ + H +K E+++ +A+ + + A+ DGI G+DGM SL S Sbjct: 39 AIVNSFTQFVPGHVHLHEIGQFVKAEIEKQGCFAAEFNTI-AIDDGIAMGHDGMLYSLPS 97 Query: 129 RDVIALSTAVGLSHNVFDGAFFLGVCDKIVPGLLIGALSFGNLASVFVPSGPMVSGIENY 188 RD+IA S ++ + D + CDKI PG+L+ A+ N+ +VFV GPM +G N Sbjct: 98 RDIIADSVEYMVNAHKADAMVCISNCDKITPGMLMAAMRL-NIPTVFVSGGPMEAGEWNG 156 Query: 189 KKAK---ARQDFAMGKINREELLKVEMQSYHDVGTCTFYGTANSNQMMMEFMGLHVANSS 245 + A A ++ E+ K+E + G C+ TANS + E +GL + + Sbjct: 157 QHLDLIDAMIKSADESVSDNEVAKIEQHACPTCGCCSGMFTANSMNCLNEAIGLALPGNG 216 Query: 246 FINPNNPLRKVLVEESAKRLASG----------KVLPLAKLIDEKSILNALIGLMATGGS 295 I + RK L +++AK + VLP + + ++ LNA+ +A GGS Sbjct: 217 TIVATHKNRKELFKDAAKLIVENAYKYYEEGDESVLPRS-IATREAFLNAMTLDIAMGGS 275 Query: 296 TNHTLHLIAIARSCGVILNWDDFDAVSNLIPLLAKVYPNGSA-DVNAFEACGGLVFVIKE 354 TN LHL+A+A G DD D +S P L KV PN V GG+V ++ E Sbjct: 276 TNTVLHLLAVAHEAGADFTMDDIDMLSRKTPCLCKVAPNTQKYHVQDVNRAGGIVAIMGE 335 Query: 355 LLKEGLLFE--------------DTHTIMDTET-QKGMQNYTKTPFLENNQLV-YKDAIN 398 L K GL+ D + I D ++ ++ Y+ + N ++ +DA Sbjct: 336 LAKGGLVDTNVRRVDGMTLAEEIDRYCITDPNVCKEAIKKYSSAAAGKFNLVLGSQDAYY 395 Query: 399 HSLNTD----ILRPVSDPFAANGGLKILKGNLGR--AVIKISAIKDEHRKVKARAIVFKT 452 L+TD +R + ++ +GGL +LKGN+ + V+K + + + K A VF + Sbjct: 396 KELDTDRAEGCIRDLQHAYSKDGGLAVLKGNIAQDGCVVKTAGVDESIWKFTGPAKVFDS 455 Query: 453 QSEFLERFKNKELERDFVAVLPFQGPKSN-GMPELHKLTTNLGALQDMGYKVALVTDGRM 511 Q + ++ V V+ +GPK GM E+ T+ + + + +G + AL+TDGR Sbjct: 456 QEAACDGILGGKVVSGDVVVITHEGPKGGPGMQEMLYPTSYIKS-RHLGKECALITDGRF 514 Query: 512 SGASGKVPSAIHLSPEGALNGAIIKIKDGDLIELDAPNNALNVLEKDFE 560 SG + + S H+SPE A G I KI+DGD+IE+D PN ++NV D E Sbjct: 515 SGGTSGL-SIGHISPEAAAGGNIGKIQDGDIIEIDIPNRSINVKLTDEE 562 Lambda K H 0.318 0.135 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: 779 Number of extensions: 41 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: 600 Length adjustment: 37 Effective length of query: 571 Effective length of database: 563 Effective search space: 321473 Effective search space used: 321473 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 24 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