Align Probable galactarate dehydratase (L-threo-forming); GalcD; EC 4.2.1.42 (uncharacterized)
to candidate 8501272 DvMF_2005 Altronate dehydratase (RefSeq)
Query= curated2:P42240 (510 letters) >FitnessBrowser__Miya:8501272 Length = 387 Score = 136 bits (343), Expect = 1e-36 Identities = 115/383 (30%), Positives = 176/383 (45%), Gaps = 33/383 (8%) Query: 117 TFEGYRNADGSAGTKNILGITTSVQCVVGVLDYAVKRIKEELLPKYPNVDDVVPLHHQYG 176 TF GYR +G G +N V+ LD E + NV + L H YG Sbjct: 5 TFLGYRRENGRVGVRN--------HVVILPLDDLSNAASEAVAN---NVKGTMALPHPYG 53 Query: 177 CGVAINAPDAVIPIRTIQNLAKHPNFGGEVMVIGLGCE--KLLPERIASENDDDILSLQD 234 D + RT+ + +PN V+VIG+ + + E IA + Sbjct: 54 R--LQFGEDLELHFRTLIGVGSNPNVAA-VVVIGIEPQWTNRIVEGIAKTGKPVAGFSIE 110 Query: 235 HRGFAAMIQSILEMAEERLIRLNSRTRVSCPVSDLVIGLQCGGSDAFSGVTANPAVGYAA 294 G I + A+E + RV CPVSDL + +CG SD SG+ +NP VG A Sbjct: 111 QNGDHNTICNASRKAKEFMHWATELQRVECPVSDLWVSTKCGESDTTSGIASNPTVGNAF 170 Query: 295 DLLVRAGATVLFSEVTEVRDAIHLLTPRAVSEEVGQSLIKEMKWYDSYLRRGDADRSAN- 353 D L G T+LF E TE+ HL+ R ++EV + ++D Y + D ++++ Sbjct: 171 DKLYEQGCTLLFGETTELTGGEHLVLERCANDEVRKQF---QFFFDRYAKLVDDHKTSDL 227 Query: 354 ----PSPGNKKGGLSNVVEKALGSVAKSG-TSPISGVLGPGERAKQKGLLFAATPASDFV 408 P+ GN +GGL+ + EKALG++ K G +P+ G L E GL F + ++ Sbjct: 228 SDSQPTKGNIEGGLTTIEEKALGNIQKIGRKAPVVGCLDKAEAPTGPGLWFMDSSSAAAE 287 Query: 409 CGTLQLAAGMNLQVFTTGRGTPYGLAAAPVLKV----STRHSLSEHWADLIDINAGRIAT 464 TL AAG + +F TG+G G PV+K+ T ++SEH ID++ I Sbjct: 288 MVTLCAAAGFVVHLFPTGQGNVIGNPILPVVKLCANPRTVRTMSEH----IDVDVSGILR 343 Query: 465 GEASIEDVGWEIFRTILDVASGR 487 E +++ G ++ + A+GR Sbjct: 344 KELTMDGAGDKLVEMAIRTANGR 366 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: 483 Number of extensions: 24 Number of successful extensions: 3 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: 510 Length of database: 387 Length adjustment: 32 Effective length of query: 478 Effective length of database: 355 Effective search space: 169690 Effective search space used: 169690 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: 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