Align 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_011383248.1 AMB_RS04115 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase
Query= metacyc::MONOMER-20632 (478 letters) >NCBI__GCF_000009985.1:WP_011383248.1 Length = 485 Score = 314 bits (805), Expect = 4e-90 Identities = 191/479 (39%), Positives = 268/479 (55%), Gaps = 22/479 (4%) Query: 5 LRHYIGGERVAADAPAESLNPSNTNDVVAKVPMGGQAEVDAAVDAARKAFPAWADASPEV 64 ++H I G +V + + +LNP+N N+V+ ++ GG+AEV AV AA++AFP WA Sbjct: 2 IKHLINGRQVESASTIANLNPAN-NEVICQIAAGGEAEVAQAVAAAKEAFPKWAGLPASQ 60 Query: 65 RSDLLDKVGSTIIARSADIGRLLAREEGKTLAEGIGETV-RAGRIFKYFAGEALRRHGQN 123 R+ LL KVG I +I +L + + G++ V RA F +FA G+ Sbjct: 61 RAKLLRKVGDLINQHVDEIAKLESLDTGQSYWRTKKMLVPRAADNFYFFADTCCHVDGET 120 Query: 124 LESTRPGVEIQTYRQAVGVYGLITPWNFPIAIPAWKAAPALAFGNTVVIKPAGPTPATAN 183 T + Y Q VGV GLI+PWN P WK AP LAFGNT V+K + +P +A+ Sbjct: 121 YP-TNDHLNYTLY-QPVGVVGLISPWNVPFMTATWKTAPCLAFGNTAVLKMSELSPLSAD 178 Query: 184 VLADIMAECGAPAGVFNMLFGRGS-MGDALIKHKDVDGVSFTGSQGVGAQVAAAAVARQA 242 L ++ E G PAGVFN++ G GS +G+AL+KH DV GVSFTGS G ++ + + Sbjct: 179 RLGQLILEAGIPAGVFNIVHGYGSAVGEALVKHPDVRGVSFTGSTATGNRIIQSGGLK-- 236 Query: 243 RVQLEMGGKNPLIVLDDADLERAVAIALDGSFFATGQRCTASSRLIVQDGIHDKFVALLA 302 + +E+GGK+P I+ DD D ERAV A+ + G+ CT +R++VQDG++D+FVA LA Sbjct: 237 KYSMELGGKSPNIIFDDCDFERAVDAAIVAVYGNNGESCTNGTRILVQDGLYDRFVAALA 296 Query: 303 EKVAALRVGDALDPNTQIGPAVSEDQMETSYRYIDIAASEGGRVVTGGDRIKLDNP---- 358 E+ + VGD LD T +GP ++ D + YI++ SEG RVV GG L P Sbjct: 297 ERTRKVVVGDPLDEATNVGPMITRDHWKKVTSYIELGISEGARVVAGG----LGTPEGLA 352 Query: 359 -----GWYVRPTLIADTQAGMRINNEEVFGPVASTIRVKSYEEALEIANGVEFGLSAGIA 413 G +VRPT++AD R+ EE+FGPVA IR K EAL+IAN +GL++ + Sbjct: 353 PHLKNGNFVRPTVLADVDNSWRVAQEEIFGPVACVIRFKDEAEALKIANATSYGLASYVW 412 Query: 414 TTSLKHARHFQRYARAGMTMVNLATAGVDYHVPFGGTKSSSYGAREQGFAAVEFFTQTK 472 T + A AG+ VN D PFGG K S G RE G + E F + K Sbjct: 413 TENGARAIRMAEGIEAGLVFVNSQNVR-DLRQPFGGIKGSGTG-REGGHYSYEAFLEVK 469 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: 583 Number of extensions: 22 Number of successful extensions: 6 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: 485 Length adjustment: 34 Effective length of query: 444 Effective length of database: 451 Effective search space: 200244 Effective search space used: 200244 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