Align Probable glucarate dehydratase; GDH; GlucD; EC 4.2.1.40 (uncharacterized)
to candidate WP_011778302.1 MVAN_RS05200 glucarate dehydratase
Query= curated2:Q9RDE9 (431 letters) >NCBI__GCF_000015305.1:WP_011778302.1 Length = 419 Score = 436 bits (1120), Expect = e-127 Identities = 225/428 (52%), Positives = 292/428 (68%), Gaps = 13/428 (3%) Query: 5 LTITAVHLTPILVADPPLLNTQGVHQPYTPRLIVEVETADGVTGVGETYGDAKYLELARP 64 + +T +TP+ ADPPLLNT GVHQPY R I++++T G+ G+GETY D ++L R Sbjct: 4 IRVTGARITPVAFADPPLLNTVGVHQPYALRAIIQLDTDAGLVGLGETYADTRHLARLRA 63 Query: 65 FAAKLVGRQVSDLNGLFTLADEVAVDSSRVFGQVDVGGLRGVQTADKLRLSVVSGFEVAC 124 A + G V LN + A SR+ G G G+ T+ + V+S FEVAC Sbjct: 64 AAEAITGLDVFALNRIR------ASIGSRLEGDTTAVGTAGMITSASVVDQVLSPFEVAC 117 Query: 125 LDALGKALGLPVHALLGGKVRDAVEYSAYLFYKWADHPEGVASEKDDWGAAVDPAGVVAQ 184 LD G++LG PV LLGG VRDAV +SAYLFYKWA HP +E D +G A+DP G+VAQ Sbjct: 118 LDVQGQSLGRPVSDLLGGAVRDAVPFSAYLFYKWAGHPN---AEPDRFGEAMDPNGLVAQ 174 Query: 185 ARAFTERYGFTSFKLKGGVFPPEEEIAAVKALAEAFPGHPLRLDPNGAWSVETSLKVAAE 244 AR + YGFT+ KLKGGVFPPEEE+AA++AL+ FPG PLRLDPN AW+ T++KVA+ Sbjct: 175 ARRIIDEYGFTAIKLKGGVFPPEEEMAAIEALSRNFPGLPLRLDPNAAWTPHTAVKVASG 234 Query: 245 LGDVLEYLEDPALGTPAMAEVAAKTGVPLATNMCVTTFAEIQEAFTKGAVQVVLSDHHYW 304 L +LEYLEDP G MAEVA + +PLATNMCV F ++ A TK AV+VVLSDHHYW Sbjct: 235 LAGILEYLEDPTPGLAGMAEVAQQAPMPLATNMCVVAFDQLAPAVTKNAVRVVLSDHHYW 294 Query: 305 GGLRNTQQLAAVCRTFGVGVSMHSNTHLGISLAAMTHVAATVPDLHHACDSHYPWQSEDV 364 GGL+ ++ LA +C TFG+G+SMHSN+HLGISLAAM H+A P+L +ACD+H+PW++EDV Sbjct: 295 GGLQRSRLLAGICDTFGLGLSMHSNSHLGISLAAMVHLAGATPNLTYACDTHWPWKTEDV 354 Query: 365 LTE-RLAFDGGKVAVSDAPGLGVALDRERLAFLHRRWLDDDGTLRDRDDAAAMRVADPEW 423 + + LAF G V V +PGLGV +D + L LH +++ +RDRDD MR DP + Sbjct: 355 VKDGALAFVDGAVPVPTSPGLGVEIDDDALDALHEQYVRCG--IRDRDDTGYMRTVDPSF 412 Query: 424 VTPSVPRW 431 P+ PRW Sbjct: 413 -EPAGPRW 419 Lambda K H 0.319 0.135 0.410 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: 543 Number of extensions: 27 Number of successful extensions: 4 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: 431 Length of database: 419 Length adjustment: 32 Effective length of query: 399 Effective length of database: 387 Effective search space: 154413 Effective search space used: 154413 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 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