Align phosphogluconate dehydratase (characterized)
to candidate GFF2902 PGA1_c29490 dihydroxy-acid dehydratase LivD
Query= CharProtDB::CH_024239 (603 letters) >FitnessBrowser__Phaeo:GFF2902 Length = 614 Score = 182 bits (463), Expect = 3e-50 Identities = 156/538 (28%), Positives = 251/538 (46%), Gaps = 45/538 (8%) Query: 68 IAIITSYNDMLSAHQPYEHYPEIIRKALHEANAVGQVAGGVPAMCDGVTQGQDGMELSLL 127 IAI+ S+ + H + +++ + + A V + + A+ DG+ G DGM SL Sbjct: 37 IAIVNSFTQFVPGHVHLKDLGQMVAREVEAAGGVAKEFNTI-AVDDGIAMGHDGMLYSLP 95 Query: 128 SREVIAMSAAVGLSHNMFDGALFLGVCDKIVPGLTMAALSFGHLPAVFVPSGPMASGL-- 185 SREVIA S ++ + D + + CDKI PG+ MAA+ ++PA+FV GPM +G Sbjct: 96 SREVIADSVEYMVNAHCADAMVCISNCDKITPGMLMAAMRL-NIPAIFVSGGPMEAGKID 154 Query: 186 ---PNKEKVRIRQLYAEGKVDRMA---LLESEAASYHAPGTCTFYGTANTNQMVVEFMGM 239 + +K+ + D M + E + G+C+ TAN+ + E +G+ Sbjct: 155 IADLDMKKIDLVDAMVAAASDTMTDEQVQHIEENACPTCGSCSGMFTANSMNCLAEALGL 214 Query: 240 QLPGSSFVHPDSPLRDALTAAAARQVTRMTGN---GNEWMPIGKMIDEKVVVNGIVAL-L 295 LPG+ R L A R++ +T G E + + I ++L + Sbjct: 215 ALPGNGSTLATHADRKHLFLEAGRKIVDITKRHYVGEEKGLLPREIATFDAFENAMSLDI 274 Query: 296 ATGGSTNHTMHLVAMARAAGIQINWDDFSDLSDVVPLMARLYPN-GPADINHFQAAGGVP 354 A GGSTN +HL+A+A + D LS VP + ++ PN + AGG+ Sbjct: 275 AMGGSTNTVLHLLAIANEGKVDFTMTDMDRLSRKVPCLCKVAPNIENVHMEDVHRAGGIF 334 Query: 355 VLVRELLKAGLLHEDVNTV----AGFGLSRYTLEPWLN---------------NGELDWR 395 ++ EL +AGLLH + +TV G ++++ ++ N E + Sbjct: 335 SILGELSRAGLLHNECSTVHSSTMGEAIAKWDIKVANNPDAEALFKAAPGGVRTTEAFSQ 394 Query: 396 EGAEKSLDSN----VIASFEQPFSHHGGTKVLSGNLGR--AVMKTSAVPVENQVIEAPAV 449 K LD++ VI S + FS GG VL GN+ R ++KT+ V A Sbjct: 395 SNRYKELDTDREGGVIRSKDHAFSQDGGLAVLFGNIARDGCIVKTAGVDDNILKFTGSAY 454 Query: 450 VFESQHDVMPAFEAGLLDRDCVVVVRHQGPKANGMPELHKLMPPLGVLLDRCF--KIALV 507 V ESQ + + VVV+R++GP+ G P + +++ P L + AL+ Sbjct: 455 VCESQDQAVNDILTSKVKEGDVVVIRYEGPR--GGPGMQEMLYPTSYLKSKGLGKACALL 512 Query: 508 TDGRLSGASGKVPSAIHVTPEAYDGGLLAKVRDGDIIRVNGQTGELTLLVDEAELAAR 565 TDGR SG + + S HV+PEA +GG + V+ GD I ++ + L V + ELAAR Sbjct: 513 TDGRFSGGTSGL-SIGHVSPEAAEGGTIGLVQQGDTIEIDIPNRTIHLAVSDEELAAR 569 Lambda K H 0.318 0.134 0.392 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: 877 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: 603 Length of database: 614 Length adjustment: 37 Effective length of query: 566 Effective length of database: 577 Effective search space: 326582 Effective search space used: 326582 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