Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate AO353_05300 AO353_05300 aldehyde dehydrogenase
Query= BRENDA::Q97UA1 (478 letters) >FitnessBrowser__pseudo3_N2E3:AO353_05300 Length = 481 Score = 357 bits (916), Expect = e-103 Identities = 190/474 (40%), Positives = 282/474 (59%), Gaps = 7/474 (1%) Query: 7 LADKWIKGSGEEYLDINPADKDHVLAKIRLYTKDDVKEAINKAVAKFDEWSRTPAPKRGS 66 + +W+ G+ E ++INP++ V+ + V AI+ A A F WS + R Sbjct: 11 IGGQWVAGA-EYSININPSELSDVIGEYAKADLAQVNAAIDAARAAFPAWSTSGIQARSD 69 Query: 67 ILLKAGELMEQEAQEFALLMTLEEGKTLKDSMFEVTRSYNLLKFYGALAFKISGKTLPSA 126 L K G + +E L+ EEGKTL +++ EV+R+ N+ KF+ ++SG LPS Sbjct: 70 ALDKVGSEILARREELGTLLAREEGKTLPEAIGEVSRAGNIFKFFAGECLRLSGDYLPSV 129 Query: 127 DPNTRIFTVKEPLGVVALITPWNFPLSIPVWKLAPALAAGNTAVIKPATKTPLMVAKLVE 186 P + +E LGVV LITPWNFP++IP WK+APALA GN V+KPA P L E Sbjct: 130 RPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVLKPAELVPGCAWALAE 189 Query: 187 VLSKAGLPEGVVNLVVGKGSEVGDTIVSDDNIAAVSFTGSTEVGKRIYKLVGNKNRMTRI 246 ++S+AG P GV NLV+G G +GD +V+ + +SFTGS VG++I V +R ++ Sbjct: 190 IISRAGFPAGVFNLVMGSGRVIGDAMVNSPKVDGISFTGSVGVGRQI--AVNCVSRQAKV 247 Query: 247 QLELGGKNALYVDKSADLTLAAELAVRGGFGLTGQSCTATSRLIINKDVYTQFKQRLLER 306 QLE+GGKN + ADL A EL+V+ F TGQ CTA+SRLI+ ++ +F + + ER Sbjct: 248 QLEMGGKNPQIILDDADLKQAVELSVQSAFYSTGQRCTASSRLIVTAGIHDKFVEAMAER 307 Query: 307 VKKWRVGPGTED-VDMGPVVDEGQFKKDLEYIEYGKNVGAKLIYGGNII--PGKGYFLEP 363 +K +VG + D+GPVV + Q ++DL+YI+ G++ GA+L+ GG ++ +GY+L P Sbjct: 308 MKSIKVGHALKSGTDIGPVVSQAQLEQDLKYIDIGQSEGARLVSGGGLVTCDTEGYYLAP 367 Query: 364 TIFEGVTSDMRLFKEEIFGPVLSVTEAKDLDEAIRLVNAVDYGHTAGIVASDIKAINEFV 423 T+F + MR+ +EEIFGPV ++ D D A+ + N ++G +AGI + +K N F Sbjct: 368 TLFADSEAAMRISREEIFGPVANIVRVADYDAALAMANDTEFGLSAGIATTSLKYANHFK 427 Query: 424 SRVEAGVIKVNKPTVGLELQAPFGGFKNSGATTWKEMGEDALEFYLKEKTVYEG 477 +AG++ VN PT G++ PFGG K S + +E G A EFY KT Y G Sbjct: 428 RHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGS-REQGRYAQEFYTVVKTSYIG 480 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: 581 Number of extensions: 18 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: 481 Length adjustment: 34 Effective length of query: 444 Effective length of database: 447 Effective search space: 198468 Effective search space used: 198468 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