Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate RR42_RS27350 RR42_RS27350 aldehyde dehydrogenase
Query= BRENDA::Q97UA1 (478 letters) >FitnessBrowser__Cup4G11:RR42_RS27350 Length = 486 Score = 375 bits (963), Expect = e-108 Identities = 194/474 (40%), Positives = 290/474 (61%), Gaps = 10/474 (2%) Query: 10 KWIKG-SGEEYLDINPADKDHVLAKIRLYTKDDVKEAINKAVAKFDEWSRTPAPKRGSIL 68 +W K SG + ++NPAD ++ + + T DD + A+ A A FD W +TP KR IL Sbjct: 16 EWSKSASGRTFDNVNPADTADIVGRFQASTADDAQAAVAAAAAAFDAWKKTPISKRAKIL 75 Query: 69 LKAGELMEQEAQEFALLMTLEEGKTLKDSMFEVTRSYNLLKFYGALAFKISGKTLPSADP 128 A + +E A++ A +T EEGK L S EV RS ++FY SG+T P DP Sbjct: 76 NGAADYLEANAEQIAEELTREEGKALNLSKDEVLRSAQTIRFYAVEGQSFSGETYPQDDP 135 Query: 129 NTRIFTVKEPLGVVALITPWNFPLSIPVWKLAPALAAGNTAVIKPATKTPLMVAKLVEVL 188 + +++ +EPLGVV +I+PWNFP+SIP K+APAL AGNT V KP++ PL +L + Sbjct: 136 DMIVYSQREPLGVVTVISPWNFPVSIPARKIAPALIAGNTVVFKPSSDAPLSGYRLAQAF 195 Query: 189 SKAGLPEGVVNLVVGKGSEVGDTIVSDDNIAAVSFTGSTEVGKRIYKLVGNKNRMTRIQL 248 +AG+P+GV+N + G+ +VG I + A+SFTGST G+ I++ V + TR Q+ Sbjct: 196 VEAGIPKGVLNFITGRAGDVGAAITEAPAVRAISFTGSTAAGQHIHRSV---SLSTRTQM 252 Query: 249 ELGGKNALYVDKSADLTLAAELAVRGGFGLTGQSCTATSRLIINKDVYTQFKQRLLERVK 308 ELGGKN L V + ADL A +L ++GG L+GQ+CT TSR+++ V + ++LL +VK Sbjct: 253 ELGGKNPLIVMEDADLDRAVDLTIKGGLSLSGQACTGTSRVLVMASVKAAYTEKLLAKVK 312 Query: 309 KWRVGPG-TEDVDMGPVVDEGQFKKDLEYIEYGKNVGAKLIYGGNIIPG----KGYFLEP 363 ++G G T +D+GP+ Q + L Y+E GK+ L GG+ + G KG+++ P Sbjct: 313 TLKIGSGMTPGMDVGPLATRKQLETVLGYVEAGKSEATHLC-GGDRLGGEPYDKGFYVSP 371 Query: 364 TIFEGVTSDMRLFKEEIFGPVLSVTEAKDLDEAIRLVNAVDYGHTAGIVASDIKAINEFV 423 +F GVT MR+ +EEIFGPV+++ E +AI N +YG +A IV S+ + ++F Sbjct: 372 AVFTGVTQQMRIAREEIFGPVIAIIEVSSYADAIAKANDTEYGLSAAIVTSNPRYAHDFA 431 Query: 424 SRVEAGVIKVNKPTVGLELQAPFGGFKNSGATTWKEMGEDALEFYLKEKTVYEG 477 +++G +K+N+ T G + APFGG K S +T++E G LEFY + KTVY G Sbjct: 432 HDIQSGTVKINRTTTGNLINAPFGGLKQSSTSTFRESGRAGLEFYTQIKTVYRG 485 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: 628 Number of extensions: 29 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 (21.6 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