Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate BPHYT_RS29875 BPHYT_RS29875 betaine-aldehyde dehydrogenase
Query= BRENDA::P05091 (517 letters) >FitnessBrowser__BFirm:BPHYT_RS29875 Length = 483 Score = 422 bits (1084), Expect = e-122 Identities = 217/459 (47%), Positives = 294/459 (64%), Gaps = 6/459 (1%) Query: 57 VNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDASHRGRLLNRLADLIERDR 116 +NP+T E I VA+G DVD AV+AARAA ++ W + + R R+L RLA L+ + Sbjct: 30 INPATEEPIALVAQGSAADVDTAVRAARAALKV---WNGIRTAERARILMRLAGLMRANL 86 Query: 117 TYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGKTIPIDGDFFSYTRHEPV 176 LAALE+LD GKP D+ + L YYAGW DK +G+ +P+ D +YT EPV Sbjct: 87 EELAALESLDAGKPIAAVMRQDIPAAIDTLEYYAGWCDKINGQVVPVRPDALTYTLREPV 146 Query: 177 GVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTALYVANLIKEAGFPPGVVN 236 GV I+PWNFPL++ WK+ PALA G +++K AE TPLTAL + L EAG PPGV+N Sbjct: 147 GVVAAIVPWNFPLMIGMWKIAPALACGCTLIVKPAEITPLTALRIGELALEAGVPPGVLN 206 Query: 237 IVPGFGPTAGAAIASHEDVDKVAFTGSTEIGR-VIQVAAGSSNLKRVTLELGGKSPNIIM 295 IV G G G A+ +H VDKV FTGS +GR ++Q AAG N KRVTLELGGKS N+I Sbjct: 207 IVTGKGRVVGDALVAHPGVDKVTFTGSPSVGRGILQGAAG--NFKRVTLELGGKSANLIF 264 Query: 296 SDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVERSVARAKSRVVGNPFDSK 355 DA++D AV A +FFN GQ C AGSR D+YDE VER ARAKS VG+P + Sbjct: 265 PDANLDNAVRAAASGIFFNTGQVCSAGSRILAHRDVYDEVVERLAARAKSIKVGDPSSRE 324 Query: 356 TEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAADRGYFIQPTVFGDVQDGMTIAKE 415 T GP + Q K +LGY+ TG+ EGA L+ GG +RG+F++PTVF +V+ M I++E Sbjct: 325 TSMGPLISAAQMKTVLGYVETGRAEGASLVTGGARVGERGFFVEPTVFANVEHEMRISQE 384 Query: 416 EIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLDKANYLSQALQAGTVWVNCYDV 475 EIFGPV +++F + + AN + Y LAA V++ D+ + + +++ L+AGTVW+N Y Sbjct: 385 EIFGPVASVIRFNDEADAIRIANGTLYSLAAGVWSADIGRVHRVARDLRAGTVWINTYGY 444 Query: 476 FGAQSPFGGYKMSGSGRELGEYGLQAYTEVKTVTVKVPQ 514 + P+GG SG GRE G+ ++ +TE K V + + Q Sbjct: 445 TDVRLPWGGSGDSGFGREHGDVAIENFTEPKAVWLAIDQ 483 Lambda K H 0.319 0.136 0.409 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: 651 Number of extensions: 25 Number of successful extensions: 3 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: 517 Length of database: 483 Length adjustment: 34 Effective length of query: 483 Effective length of database: 449 Effective search space: 216867 Effective search space used: 216867 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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