Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate 6939185 Sama_3279 dihydroxy-acid dehydratase (RefSeq)
Query= BRENDA::Q1PAG1 (608 letters) >FitnessBrowser__SB2B:6939185 Length = 618 Score = 211 bits (537), Expect = 7e-59 Identities = 183/587 (31%), Positives = 277/587 (47%), Gaps = 55/587 (9%) Query: 68 VAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEAGMELSLP 127 +AI +S+ + H + + A+ E G + + T A+ DG+ G GM SLP Sbjct: 37 IAIANSFTQFVPGHVHLKDMGSLVASAIEEAGGIAK-EFNTIAVDDGIAMGHGGMLYSLP 95 Query: 128 SREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMPSG--- 184 SRE+IA S ++ + DA + + CDKI PG++M ALR ++P +FV GGPM +G Sbjct: 96 SRELIADSVEYMVNAHCADALVCISNCDKITPGMLMAALRL-NIPVVFVSGGPMEAGKTK 154 Query: 185 ISNK----EKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240 +S+K + D A+ + + + + E + + G+C+ TAN+ L E +GL Sbjct: 155 LSDKLIKLDLVDAMVAAADDRISDADSEKIERSACPTCGSCSGMFTANSMNCLTEALGLS 214 Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQ-----SGNFTPIGEIVDERSLVNSIVALH 295 LPG + R L EA ++V +L K+ + P I ++ N++ Sbjct: 215 LPGNGSMLATHADRRELFLEAGRRVMKLAKRYYGDDDASVLP-RSIASFKAFENAMALDV 273 Query: 296 ATGGSTNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPN-GKADINHFQAAGGMA 354 A GGS+N LH+ A AQ A + T D+ +S VP L V P+ K + AGG+ Sbjct: 274 AMGGSSNTVLHLLAAAQEAEVDFTMDDIDRISRKVPHLCKVAPSTPKYHMEDVHRAGGVM 333 Query: 355 FLIRELLEAGLLHEDVNTVAGR-GLSRYTQEPF---LDNGKLV---WRDGPI-------- 399 ++ EL AGLLH DVN VA G + E F L + V +R GP Sbjct: 334 AILGELDRAGLLHTDVNHVASEDGTLKSVLERFDVVLTKDEKVHEFFRAGPAGIPTTRAF 393 Query: 400 ------ESLD----ENILRPVARAFSPEGGLRVMEGNLGRG--VMKVSAVALQHQIVEAP 447 ++LD E +R AFS EGGL V+ GNL ++K + V + Sbjct: 394 SQSCRWDTLDDDRREGCIRSREFAFSQEGGLAVLSGNLAENGCIVKTAGVDESNLKFSGV 453 Query: 448 AVVFQDQQDLADAFKAGELEKDFVAVMRFQGPRSNGMPELHKMTPFLGVLQDRGF--KVA 505 A V++ Q+D GE+ V V+RF+GP+ G P + +M L+ RG + A Sbjct: 454 ARVYESQEDAVAGILGGEVVAGDVVVIRFEGPK--GGPGMQEMLYPTSYLKSRGLGTQCA 511 Query: 506 LVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRDGDIIRVDGVKGTLELKVDADEFAAR 565 L+TDGR SG + + HVSPEA GG + + +GD I +D +++L V E +R Sbjct: 512 LITDGRFSGGTSGLSIG-HVSPEAASGGTIGLIENGDRIDIDIPGRSIKLLVSDAELESR 570 Query: 566 EPAKGLLG-------NNVGSGRELFGFMRMAFSSAEQGASAFTSALE 605 A G + V M +SA++GA S LE Sbjct: 571 RAAMNAKGPLAWKPLSRVRPVSMALKAYAMLATSADKGAVRDVSKLE 617 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: 911 Number of extensions: 52 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: 608 Length of database: 618 Length adjustment: 37 Effective length of query: 571 Effective length of database: 581 Effective search space: 331751 Effective search space used: 331751 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