Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate BPHYT_RS09900 BPHYT_RS09900 aldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >FitnessBrowser__BFirm:BPHYT_RS09900 Length = 492 Score = 400 bits (1027), Expect = e-116 Identities = 218/481 (45%), Positives = 295/481 (61%), Gaps = 10/481 (2%) Query: 20 PTGLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHS-SWSTS 78 P +FIN E S + KTF +P+T EEI Q+ +A DID AV + AAF S +W Sbjct: 11 PHTMFINGEKTGSAAGKTFPVFNPATAEEIAQIPDASEADIDHAVRTSKAAFESDAWRRM 70 Query: 79 DPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKG-DVALTAAYFRSCAGWTDKI 137 P VR +L KLADL++ H+D LA +E L+ GK + SK +VA + + R AGW KI Sbjct: 71 PPAVREGLLLKLADLVERHSDELATLETLNQGKLIGFSKMLEVAGSVQWLRYMAGWATKI 130 Query: 138 KGSVIETG-----DTHFNY-TRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKT 191 +GS + T +N T+R P GV I+PWNFPLLMA WK+ P L GCT VLK Sbjct: 131 EGSTFDLSIPFPPGTRYNASTKRVPAGVVAAIVPWNFPLLMAVWKIAPALACGCTVVLKP 190 Query: 192 AESTPLSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHI 251 AE TPL+A+ LA L EAG P GV NVV+G G TAGA + HP +KKV FTGST GR I Sbjct: 191 AEETPLTAIRLAELAHEAGFPAGVFNVVTGRGETAGAALVRHPLVKKVTFTGSTEVGRII 250 Query: 252 MKAAAESNLKKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEG 311 + A+ +LK+ +LELGGKSP IV DD D + I+ IF+N G+VC AGSR+YV Sbjct: 251 GRQCAD-DLKRASLELGGKSPVIVLDDCDPRKAIEGAAGAIFFNHGQVCTAGSRLYVARS 309 Query: 312 IYDKIVSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGER 371 IYD++V A+ + +G F T MG S DK+ I GK EG +++ R Sbjct: 310 IYDEVVQGIAAVADGITLGSGFDAATQMGPMVSARHRDKVAGMIAQGKDEGGEIVSRDAR 369 Query: 372 FGNKGYFIKPTIFGD-VKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVH 430 +GYF++PT+ + + +V++E+FGPV+ + ++EV+A AN SEYGL A V Sbjct: 370 VEREGYFVRPTVIANRACKPLAVVKEEVFGPVLVAMPYDDLDEVLAQANASEYGLGASVW 429 Query: 431 TTNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVR 490 T L A+ + + I +GT+WVNT+N P +PFGG+ SGIGRE G+ +++YT+ K+V Sbjct: 430 TNQLDKALRLVDGIEAGTVWVNTHNMVDPAMPFGGFKASGIGREHGKSIIESYTESKSVC 489 Query: 491 I 491 I Sbjct: 490 I 490 Lambda K H 0.316 0.133 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: 608 Number of extensions: 35 Number of successful extensions: 6 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: 495 Length of database: 492 Length adjustment: 34 Effective length of query: 461 Effective length of database: 458 Effective search space: 211138 Effective search space used: 211138 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