Align Probable glucarate dehydratase; GDH; GlucD; EC 4.2.1.40 (uncharacterized)
to candidate BPHYT_RS31145 BPHYT_RS31145 glucarate dehydratase
Query= curated2:Q9RDE9 (431 letters) >FitnessBrowser__BFirm:BPHYT_RS31145 Length = 424 Score = 402 bits (1033), Expect = e-116 Identities = 214/424 (50%), Positives = 276/424 (65%), Gaps = 8/424 (1%) Query: 1 MTRDLTITAVHLTPILVADPPLLNTQGVHQPYTPRLIVEVETADGVTGVGETYGDAKYLE 60 MTRD+T+T V +TPI D PLLN G+H+P+ R IVE+ET+DG G+ ETYGD L Sbjct: 1 MTRDITVTQVRITPIAFRDGPLLNAAGIHEPWALRAIVELETSDGRVGISETYGDEPMLR 60 Query: 61 LARPFAAKLVGRQVSDLNGLFTLADEVAVDSSRVFGQVDVGGLRGVQTADKLRLSVVSGF 120 + A ++G DLN + SS G + A K V+S Sbjct: 61 VLEQAKALVIGLSPFDLNRMEERVRAAIKPSSGAIEFELAPGSHSAKNAPK----VISTL 116 Query: 121 EVACLDALGKALGLPVHALLGGKVRDAVEYSAYLFYKWADHPEGVASEKDDWGAAVDPAG 180 EVA LD G+ +G P+ LLGGKVRDAV YSAYLF+K+A+H + + D WG + Sbjct: 117 EVAMLDLQGQIVGAPIVDLLGGKVRDAVPYSAYLFFKYAEHIDKPYAP-DAWGEGLSADQ 175 Query: 181 VVAQARAFTERYGFTSFKLKGGVFPPEEEIAAVKALAEAFPGHPLRLDPNGAWSVETSLK 240 +VAQAR + YGF S KLKGGVF P EIA ++AL AFPG PLRLDPN W++ETS+ Sbjct: 176 IVAQARRMIDLYGFQSIKLKGGVFEPAHEIACMRALHRAFPGVPLRLDPNANWTLETSIA 235 Query: 241 VAAELGDVLEYLEDPALGTPAMAEVAAKTGVPLATNMCVTTFAEIQEAFTKGAVQVVLSD 300 A EL ++LEY EDP G MAE+A T +PLATNM +TT + + G+V+V+LSD Sbjct: 236 AAPELDELLEYYEDPCPGLAGMAELAKHTRLPLATNMVITTMEDFRRGAEMGSVKVLLSD 295 Query: 301 HHYWGGLRNTQQLAAVCRTFGVGVSMHSNTHLGISLAAMTHVAATVPDLHHACDSHYPWQ 360 HHYWGGLR TQ LA +C+ + +G+SMHSN+HLGISL AMTHVAA++P+L +ACD+HYPWQ Sbjct: 296 HHYWGGLRATQTLARMCKLWDLGMSMHSNSHLGISLMAMTHVAASIPNLTYACDTHYPWQ 355 Query: 361 SEDVLT-ERLAFDGGKVAVSDAPGLGVALDRERLAFLHRRWLDDDGTLRDRDDAAAMRVA 419 E+V+ R++FD G V V APGLGV LDRERLA LH ++L +R+RDD M+ Sbjct: 356 EEEVIKGGRVSFDNGAVRVPSAPGLGVELDRERLAELHAQYLTCG--VRNRDDLKQMQKY 413 Query: 420 DPEW 423 DP + Sbjct: 414 DPSF 417 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: 498 Number of extensions: 20 Number of successful extensions: 5 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: 424 Length adjustment: 32 Effective length of query: 399 Effective length of database: 392 Effective search space: 156408 Effective search space used: 156408 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 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