Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate GFF501 PGA1_c05130 aldehyde dehydrogenase
Query= BRENDA::Q97UA1 (478 letters) >FitnessBrowser__Phaeo:GFF501 Length = 476 Score = 327 bits (837), Expect = 7e-94 Identities = 179/457 (39%), Positives = 262/457 (57%), Gaps = 5/457 (1%) Query: 21 DINPADKDHVLAKIRLYTKDDVKEAINKAVAKFDEWSRTPAPKRGSILLKAGELMEQEAQ 80 +INP+D VL +D++ AI A W+ + +R +L G + Sbjct: 20 NINPSDTQDVLGYAANSPAEDMERAIAAARDAAPGWASSTPQQRFDVLDAIGTEILARKA 79 Query: 81 EFALLMTLEEGKTLKDSMFEVTRSYNLLKFYGALAFKISGKTLPSADPNTRIFTVKEPLG 140 E L++ EEGKTL + + E R+ + KF+ + +G+ L S P + + P+G Sbjct: 80 ELGKLLSREEGKTLPEGIGEAARAGQIFKFFAGETLRQAGEILGSVRPGVGVEVTRSPVG 139 Query: 141 VVALITPWNFPLSIPVWKLAPALAAGNTAVIKPATKTPLMVAKLVEVLSKAGLPEGVVNL 200 VV LITPWNFP++IP WK+APALA G+ V+KPA TP L E+++++GLPEGV N+ Sbjct: 140 VVGLITPWNFPIAIPAWKIAPALAYGDAVVLKPAELTPGCAHALAEIINRSGLPEGVFNI 199 Query: 201 VVGKGSEVGDTIVSDDNIAAVSFTGSTEVGKRIYKLVGNKNRMTRIQLELGGKNALYVDK 260 V G GS VG T+V ++ A+SFTGS E G I G + + ++QLE+GGKN + V Sbjct: 200 VFGTGSTVGQTLVQSRHVDAISFTGSVETGSAIAAACGAQRK--KLQLEMGGKNPMVVLD 257 Query: 261 SADLTLAAELAVRGGFGLTGQSCTATSRLIINKDVYTQFKQRLLERVKKWRVGPGTED-V 319 ADL A + ++ G F TGQ CTA+SRLI+ + ++ +F L ER+ RVG +D Sbjct: 258 DADLETAVDASLNGAFFSTGQRCTASSRLIVTEGIHDRFVAALGERMTGLRVGNALDDST 317 Query: 320 DMGPVVDEGQFKKDLEYIEYGKNVGAKLIYGGNIIPG-KGYFLEPTIFEGVTSDMRLFKE 378 +GPVVDE Q +KDL Y++ + G +++ G + KG++L P + ++DMR+ +E Sbjct: 318 QIGPVVDERQLEKDLYYLDVAASEGGQVLGGQTLQRSTKGFYLAPALVTETSNDMRINQE 377 Query: 379 EIFGPVLSVTEAKDLDEAIRLVNAVDYGHTAGIVASDIKAINEFVSRVEAGVIKVNKPTV 438 E+FGP+ SV D DEA+ + N +G +AGI +K F + EAG+ VN PT Sbjct: 378 EVFGPLASVIRVADYDEALVVANDTPFGLSAGICTGSLKYATHFKAHAEAGMAMVNLPTA 437 Query: 439 GLELQAPFGGFKNSGATTWKEMGEDALEFYLKEKTVY 475 G++ PFGG K S +E G A EFY K KT Y Sbjct: 438 GVDYHVPFGGTKGSSFGA-REQGSHAKEFYTKVKTAY 473 Lambda K H 0.316 0.135 0.389 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: 595 Number of extensions: 34 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: 478 Length of database: 476 Length adjustment: 33 Effective length of query: 445 Effective length of database: 443 Effective search space: 197135 Effective search space used: 197135 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 (21.6 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