Align 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate SMa1415 SMa1415 aldehyde dehydrogenase
Query= metacyc::MONOMER-20632 (478 letters) >FitnessBrowser__Smeli:SMa1415 Length = 498 Score = 284 bits (727), Expect = 4e-81 Identities = 177/436 (40%), Positives = 247/436 (56%), Gaps = 7/436 (1%) Query: 42 EVDAAVDAARKAFP--AWADASPEVRSDLLDKVGSTIIARSADIGRLLAREEGKTLAEGI 99 +++AAV AAR+AF W+ R+ +L +V + R ++ E GK +A+ Sbjct: 53 DLNAAVAAARRAFEDRRWSGLPGGSRASVLLRVAEILRTRRDELAYWETLENGKPIAQAR 112 Query: 100 GETVRAGRIFKYFAGEALRRHGQNLESTRPGVEIQTYRQAVGVYGLITPWNFPIAIPAWK 159 GE F+ AG A HG + S G+ R+ +GV GLITPWNFP I + Sbjct: 113 GEIDHCIACFEVGAGAARLLHGDSFNSLGDGLFGMVLREPIGVVGLITPWNFPFLILCER 172 Query: 160 AAPALAFGNTVVIKPAGPTPATANVLADIMAECGAPAGVFNMLFGRG-SMGDALIKHKDV 218 LA G T+V+KP+ T AT +LA+++AE G P GV+N++ G G ++G A+ +H D+ Sbjct: 173 VPFILASGCTMVVKPSEVTSATTLILAEVLAEAGLPDGVYNVITGSGRTIGQAMSEHPDI 232 Query: 219 DGVSFTGSQGVGAQ-VAAAAVARQARVQLEMGGKNPLIVLDDADLERAVAIALDGSFFAT 277 D +SFTGS VG V AAA + ++ LE+GGKNP+IV D+DLE A A G F T Sbjct: 233 DMLSFTGSTAVGRSCVHAAADSNFKKLGLELGGKNPIIVFADSDLEDAADGAAFGISFNT 292 Query: 278 GQRCTASSRLIVQDGIHDKFVALLAEKVAALRVGDALDPNTQIGPAVSEDQMETSYRYID 337 GQ C +SSRLIV+ + +F ALLAEK+ +RVGD LD TQ+G +E Q T YI Sbjct: 293 GQCCVSSSRLIVERSVAREFEALLAEKMKRIRVGDPLDETTQVGAITTEAQNTTILDYIA 352 Query: 338 IAASEGGRVVTGGDRIKLDNPGWYVRPTLIADTQAGMRINNEEVFGPVASTIRVKSYEEA 397 +EG +VTGG I L G Y+ PTL + M I +E+FGPV ++ + E+A Sbjct: 353 KGKTEGAELVTGGTAIDLGR-GQYIAPTLFSGVSREMAIARDEIFGPVLCSMTFDTVEQA 411 Query: 398 LEIANGVEFGLSAGIATTSLKHARHFQRYARAGMTMVNLATAGVDYHVPFGGTKSSSYGA 457 +E+AN +GL+A + T ++ A R RAG VN AG +P GG K S +G Sbjct: 412 VELANDTVYGLAASVWTKNIDKALTVTRRVRAGRFWVNTMMAG-GPEMPLGGFKQSGWG- 469 Query: 458 REQGFAAVEFFTQTKT 473 RE G VE +TQ K+ Sbjct: 470 REAGMYGVEEYTQVKS 485 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: 600 Number of extensions: 24 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: 498 Length adjustment: 34 Effective length of query: 444 Effective length of database: 464 Effective search space: 206016 Effective search space used: 206016 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