Align Probable galactarate dehydratase (L-threo-forming); GalcD; EC 4.2.1.42 (uncharacterized)
to candidate CA265_RS04670 CA265_RS04670 altronate hydrolase
Query= curated2:P42240 (510 letters) >FitnessBrowser__Pedo557:CA265_RS04670 Length = 545 Score = 224 bits (572), Expect = 5e-63 Identities = 167/537 (31%), Positives = 245/537 (45%), Gaps = 76/537 (14%) Query: 12 LYIKVHEIDNTAIIVNDGGLPKGTVF---SCGLVLEEDVPQGHKVALTDLNQGDEIVRYG 68 L IK++ DN + + D LPK T V +++P HK + D+ GDE++ YG Sbjct: 4 LVIKINHADNVLVALQD--LPKNTEIVHEGNTYVTVDEIPAKHKFFMQDMKAGDEVMMYG 61 Query: 69 EVIGFADETIKRGSWIREALVRMPAPP-----------ALDDLPLANRVPQPRPPLEGYT 117 ++G +K G + + A P A D ANR + Sbjct: 62 VLVGKVQFDVKAGMRMNVENTKHAAEPFAYRNVNYKWEAPDVSKYANR-----------S 110 Query: 118 FEGYRNADGSAGTKNILGITTSVQC-----------VVGVLDYAV----KRIKEELLPKY 162 F GY +G GT N +V C + L YAV K +L+ Y Sbjct: 111 FNGYHRKNGEVGTANYWLFIPTVFCENRNLDIIKESLYSELGYAVDDKYKSYTHKLVQAY 170 Query: 163 ----------------------PNVDDVVPLHHQYGCGVAINAPDAVIPIRTIQNLAKHP 200 NVD + L H GCG D + + + A HP Sbjct: 171 ENGEDIHNISFEPKVDKASRTFKNVDGIKFLTHNGGCGGTRQDSDTL--SKLLAAYAHHP 228 Query: 201 NFGGEVMVIGLGCEKLLPE-----RIASENDDD----ILSLQDHRGFAAMIQSILEMAEE 251 N G + V+ LGC+ L E A + D D I Q + +IQ+ + E Sbjct: 229 NVAG-ITVLSLGCQHLQVEDFKRDLFALDPDFDKPLLIFEQQKAQSEEELIQNSIRSTFE 287 Query: 252 RLIRLNSRTRVSCPVSDLVIGLQCGGSDAFSGVTANPAVGYAADLLVRAGATVLFSEVTE 311 L+ +N + R + P+S + +G++CGGSD FSG++ANP+VGY ADLLV GA VL +E E Sbjct: 288 GLMFINKQARAAAPLSKMCVGVKCGGSDGFSGISANPSVGYCADLLVALGAKVLLAEFPE 347 Query: 312 VRDAIHLLTPRAVSEEVGQSLIKEMKWYDSYLRRGDADRSANPSPGNKKGGLSNVVEKAL 371 + + R+V + + I+ M YD + + NPSPGN K GL K+ Sbjct: 348 LCGVEQEMIDRSVDQPTAEKFIRLMTEYDDLAHKVGSGFYMNPSPGNIKDGLITDAIKSA 407 Query: 372 GSVAKSGTSPISGVLGPGERAKQKGLLFAATPASDFVCGTLQLAAGMNLQVFTTGRGTPY 431 G+ K+G++PI VL E A + GL TP +D T + AAG L +FTTG GTP Sbjct: 408 GAARKAGSAPIVDVLDYTEPATKPGLSLVCTPGNDVEATTGKAAAGATLILFTTGLGTPT 467 Query: 432 GLAAAPVLKVSTRHSLSEHWADLIDINAGRIATGEASIEDVGWEIFRTILDVASGRK 488 G P +KV+T L++ +D+IDI+ G + GE +I ++G +I + VASG + Sbjct: 468 GNPVCPTIKVATNSILAKRMSDIIDIDTGAVINGEKTINEMGEDILEYCIKVASGEE 524 Lambda K H 0.318 0.136 0.406 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: 661 Number of extensions: 34 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 510 Length of database: 545 Length adjustment: 35 Effective length of query: 475 Effective length of database: 510 Effective search space: 242250 Effective search space used: 242250 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