Align Galactarate dehydratase (L-threo-forming); GalcD; EC 4.2.1.42 (characterized)
to candidate Echvi_3632 Echvi_3632 Altronate dehydratase
Query= SwissProt::P39829 (523 letters) >FitnessBrowser__Cola:Echvi_3632 Length = 548 Score = 212 bits (539), Expect = 3e-59 Identities = 161/537 (29%), Positives = 244/537 (45%), Gaps = 64/537 (11%) Query: 16 IKVHDTDNVAIIVNDNGLKAGTRFP---DGLELIEHIPQGHKVALLDIPANGEIIRYGEV 72 +K+H DNV + + D LKAG + + + L + HK A + +I YG + Sbjct: 6 LKIHPKDNVLVALTD--LKAGEQIEFEGNEITLTHDVKAKHKFAEAAFATDEDIYMYGII 63 Query: 73 IGYAVRAIPRGSWIDESMVVLPEAPPLHTLPLATKV----PEPLPPLEGY---TFEGYRN 125 G A+ AI +G VL H T V P P + + TF GY Sbjct: 64 CGKAMNAIAKGE-------VLTTQNVAHKTSEFTGVRDFKPWNAPDVSKWADRTFMGYHR 116 Query: 126 ADGSVGTKNLLGITTSVHCVAGVVDYV--------------------------------- 152 DG VGT N + V C ++ + Sbjct: 117 EDGQVGTANYWLVIPLVFCENRNIEIMKNAFVEELGFAKPNKYKSFVKQMKDLYTQGKKE 176 Query: 153 ------VKIIERDLLPK-YPNVDGVVGLNHLYGCGVAINAPAAVVPIRTIHNISLNPNFG 205 V+ E+D + + N+DG+ L H GCG I + ++ I NPN Sbjct: 177 EIATLSVETAEQDGESRIFKNIDGIKFLTHQAGCG-GIRQDSEML-CGLIAGYINNPNVA 234 Query: 206 GEVMVIGLGCEKLQPERLLTGTDDVQAIPVESASIVSLQDEKHVGFQSMVEDILQIAERH 265 G ++ LGC+ QP L D + P ++ L+ ++ +++ + +Q Sbjct: 235 GAT-ILSLGCQNAQPSILREKLDKIN--PDLKKPVIILEQQQEGTENTLLTNAIQKTFLA 291 Query: 266 LQKLNQRQRETCPASELVVGMQCGGSDAFSGVTANPAVGYASDLLVRCGATVMFSEVTEV 325 L +Q +R+ P S+L VG++CGGSD FSG++ANP+VG+ASDL+V G + SE E+ Sbjct: 292 LTDADQLERQPAPLSKLTVGLECGGSDGFSGISANPSVGHASDLVVALGGKTILSEFPEL 351 Query: 326 RDAIHLLTPRAVNEEVGKRLLEEMEWYDNYLNMGKTDRSANPSPGNKKGGLANVVEKALG 385 L R +E + + M Y + NPSPGN K GL K+ G Sbjct: 352 CGVEQELINRCTTDESADKFVTLMRAYAASAEAVGSGFDMNPSPGNIKDGLITDAMKSAG 411 Query: 386 SIAKSGKSAIVEVLSPGQRPTKRGLIYAATPASDFVCGTQQVASGITVQVFTTGRGTPYG 445 + K G S IV+VL + TK GL TP +D T SG V +FTTG GTP G Sbjct: 412 AAKKGGTSPIVDVLDYAEYVTKPGLNLLCTPGNDVESTTAMAGSGANVILFTTGLGTPTG 471 Query: 446 LMAVPVIKMATRTELANRWFDLMDINAGTIATGEETIEEVGWKLFHFILDVASGKKK 502 PV+K+++ LA + D++DIN G + +G++TI+++G ++ I++VASG KK Sbjct: 472 NPVTPVLKVSSNHILAEKMDDIIDINTGGVISGDKTIDQMGEEILEHIIEVASGNKK 528 Lambda K H 0.317 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: 685 Number of extensions: 38 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 523 Length of database: 548 Length adjustment: 35 Effective length of query: 488 Effective length of database: 513 Effective search space: 250344 Effective search space used: 250344 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: 52 (24.6 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