Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate Ac3H11_3961 Aldehyde dehydrogenase B (EC 1.2.1.22)
Query= BRENDA::Q97UA1 (478 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3961 Length = 512 Score = 344 bits (882), Expect = 5e-99 Identities = 187/463 (40%), Positives = 268/463 (57%), Gaps = 9/463 (1%) Query: 19 YLDINPADKDHVLAKIRLYTKDDVKEAINKAVAKFDEWSRTPAPKRGSILLKAGELMEQE 78 Y + NP+D V+ + +++ +A+ A A F WS + +R IL G + Sbjct: 50 YQNTNPSDTRDVIGDYAVASREQALDAVAAAHAAFPAWSLSTPQQRFDILDAVGNEIIAR 109 Query: 79 AQEFALLMTLEEGKTLKDSMFEVTRSYNLLKFYGALAFKISGKTLPSADPNTRIFTVKEP 138 E L+ EEGKTL +++ EV R+ + KF+ A + G+ +PS P I +EP Sbjct: 110 KAELGDLLAREEGKTLPEAIGEVGRAAAIFKFFAGEALRPGGEVMPSVRPGVGIEITREP 169 Query: 139 LGVVALITPWNFPLSIPVWKLAPALAAGNTAVIKPATKTPLMVAKLVEVLSKAGLPEGVV 198 LG + +ITPWNFP++IP WK+APALA GN V KPA P L ++L +AGLP GV Sbjct: 170 LGTIGIITPWNFPIAIPAWKIAPALAYGNCVVFKPAEVVPGSAWALADILHRAGLPAGVF 229 Query: 199 NLVVGKGSEVGDTIVSDDNIAAVSFTGSTEVGKRIYKLVGNKNRMTRIQLELGGKNALYV 258 NLV+G+GS+VG ++ D+ IA VSFTGS G+R+ R ++QLE+GGKN V Sbjct: 230 NLVMGRGSDVGAVLLEDERIAGVSFTGSVGTGQRV--AAACVPRGAKVQLEMGGKNPFVV 287 Query: 259 DKSADLTLAAELAVRGGFGLTGQSCTATSRLIINKDVYTQFKQRLLERVKKWRVGPGTE- 317 ADL +A A+ GF TGQ CTA+SR+I+ + ++ +F ++E++K +V + Sbjct: 288 LDDADLNVAVGAAINSGFFSTGQRCTASSRVIVTEGIHDRFVAAMVEKMKTLKVDDARKA 347 Query: 318 DVDMGPVVDEGQFKKDLEYIEYGKNVGAKLIYGG-----NIIPGKGYFLEPTIFEGVTSD 372 D+GPVVD+ Q +DLEYI G+ GAKL YGG N G++L P +F T Sbjct: 348 GTDIGPVVDDRQLAQDLEYIGIGQQEGAKLAYGGEALEKNADGAPGFYLRPALFTETTPG 407 Query: 373 MRLFKEEIFGPVLSVTEAKDLDEAIRLVNAVDYGHTAGIVASDIKAINEFVSRVEAGVIK 432 MR+ +EEIFGPV+SV AK+ +EA+ L N +G +GI + +K F +AG++ Sbjct: 408 MRINREEIFGPVVSVLRAKNYEEALALANDTPFGLASGIATTSLKHATHFKRHAQAGMVM 467 Query: 433 VNKPTVGLELQAPFGGFKNSGATTWKEMGEDALEFYLKEKTVY 475 VN PT G++ PFGG K+S +E G A EFY KT Y Sbjct: 468 VNLPTAGVDYHVPFGGRKSSSYGP-REQGRYAAEFYTTVKTAY 509 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: 653 Number of extensions: 23 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: 512 Length adjustment: 34 Effective length of query: 444 Effective length of database: 478 Effective search space: 212232 Effective search space used: 212232 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