Align 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_012756139.1 RLEG_RS02225 aldehyde dehydrogenase
Query= metacyc::MONOMER-20632 (478 letters) >NCBI__GCF_000023185.1:WP_012756139.1 Length = 486 Score = 314 bits (804), Expect = 5e-90 Identities = 191/477 (40%), Positives = 277/477 (58%), Gaps = 12/477 (2%) Query: 4 TLR--HYIGGERVAADAPA--ESLNPSNTNDVVAKVPMGGQAEVDAAVDAARKAFPAWAD 59 TLR ++I G+ A + E NP ++ +++ V Q +V+ A+ AAR AFPAWA+ Sbjct: 3 TLRILNWINGQASHASSEGWLEKFNP-HSGELLYHVADSSQDDVEQAITAARSAFPAWAE 61 Query: 60 ASPEVRSDLLDKVGSTIIARSADIGRLLAREEGKTLAEGIGETVRAGRIFKYFAGEALRR 119 +P R +L + + + RS ++ +A E GK + GET A +YFAGE +R Sbjct: 62 LTPVKRGQILMDIVALMKRRSDELAECIALETGKPPQDAKGETGGAIMQAEYFAGEGMRL 121 Query: 120 HGQNLESTRPGVEIQTYRQAVGVYGLITPWNFPIAIPAWKAAPALAFGNTVVIKPAGPTP 179 + ++L S PG T RQ GV GLI P N PIA AWK PAL GNTVV+K A +P Sbjct: 122 YARSLTSGTPGKYSHTVRQPRGVAGLIVPANTPIANIAWKTFPALICGNTVVLKAAEDSP 181 Query: 180 ATANVLADIMAECGAPAGVFNMLFGRGS-MGDALIKHKDVDGVSFTGSQGVGAQVAAAAV 238 A + A++ E G P GVFN++ GRG G L+ + VD +SFTGS GVG ++A A Sbjct: 182 RIAQLFAELTKEAGLPDGVFNVVHGRGEPAGSTLVTDERVDIISFTGSTGVGRRIAEVAG 241 Query: 239 ARQARVQLEMGGKNPLIVLDDADLERAVAIALDGSFFATGQRCTASSRLIVQDGIHDKFV 298 R AR+ LE+GGKNP +V DDADL++AV A +F GQRC A SR++V ++++F Sbjct: 242 KRLARISLELGGKNPFVVCDDADLDQAVHWAALSAFSNAGQRCAAGSRMLVFKSVYEEFR 301 Query: 299 ALLAEKVAALRVGDALDPNTQIGPAVSEDQMETSYRYIDIAASEGGRVVTGG---DRIKL 355 L K +L++G A +GP VS Q ++ I+ A +GG+V+ GG D +L Sbjct: 302 DRLTAKARSLKLGVA--AGCDLGPLVSLRQQQSVLSAIERAKEQGGQVLCGGRTPDAPEL 359 Query: 356 DNPGWYVRPTLIADTQAGMRINNEEVFGPVASTIRVKSYEEALEIANGVEFGLSAGIATT 415 G+YV PT+I ++ +EVFGPV + V S EAL++AN E+GL+A + T Sbjct: 360 AG-GYYVEPTVIDGLATTSDLSCKEVFGPVTTLHPVGSMTEALDVANATEYGLTAAVHTR 418 Query: 416 SLKHARHFQRYARAGMTMVNLATAGVDYHVPFGGTKSSSYGAREQGFAAVEFFTQTK 472 ++ A F + +AG+ VN+ T G + H+PFGG SS G RE G A++ +++ K Sbjct: 419 NVDRAMWFAQRVKAGVANVNMGTYGSEPHMPFGGFGSSGNGTREPGVEALDVYSELK 475 Lambda K H 0.317 0.133 0.384 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: 585 Number of extensions: 25 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: 478 Length of database: 486 Length adjustment: 34 Effective length of query: 444 Effective length of database: 452 Effective search space: 200688 Effective search space used: 200688 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 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