Align aldehyde dehydrogenase ALDH; EC 1.2.1.3 (characterized)
to candidate WP_052594900.1 VV02_RS21400 aldehyde dehydrogenase family protein
Query= CharProtDB::CH_007936 (497 letters) >NCBI__GCF_001190945.1:WP_052594900.1 Length = 494 Score = 372 bits (955), Expect = e-107 Identities = 193/473 (40%), Positives = 294/473 (62%), Gaps = 7/473 (1%) Query: 21 LFINNEFVKGVEGKTFQVINPSNEKVITSVHEATEKDVDVAVAAARAAFE-GPWRQVTPS 79 L+I ++V +G T ++ NP+N +V V EAT D AVAAAR+AF+ G W + Sbjct: 8 LYIAGDWVHSSDGGTRELTNPANGEVFAVVDEATPADATRAVAAARSAFDQGDWPATPVN 67 Query: 80 ERGILINKLADLMERDIDTLAAIESLDNGKAFTMAKVDLANSIGCLRYYAGWADKIHGQT 139 ER L++++ADL+ERD + LA IE+ D GK +++D+ + + RYY+ + Sbjct: 68 ERAALLDRIADLLERDKEALARIETEDTGKTLVESRIDIDDVVSVFRYYSRLVGIESDRL 127 Query: 140 IDT-NPETLTYTRHEPVGVCGQIIPWNFPLLMWSWKIGPAVAAGNTVVLKTAEQTPLSAL 198 +D +P+ ++ EP+GVC I PWN+PLL SWK+ PA+AAG T+V K +E TPLS + Sbjct: 128 VDVGDPDVMSTVVREPIGVCVLIAPWNYPLLQMSWKVAPALAAGCTMVAKPSEVTPLSTI 187 Query: 199 YAAKLIKEAGFPAGVINVISGFGRTAGAAISSHMDIDKVAFTGSTLVGRTILQAAAKSNL 258 +LI+EAG PAGV+N++ G G T GAA++ D+D ++FTG GR + +AAA+ + Sbjct: 188 AFVRLIEEAGAPAGVVNLVQGSGATLGAALTETPDVDLISFTGGLATGRIVAKAAAQ-QV 246 Query: 259 KKVTLELGGKSPNIVFDDADIDNAISWANFGIFFNHGQCCCAGSRILVQEGIYDKFVARF 318 + +ELGGK+P+IVF D + ++++ G+F + GQ C AG+R++++E I D FVA Sbjct: 247 TRCAVELGGKNPHIVFADTEWESSVDQVLTGVFLHSGQVCSAGTRLIIEESIADDFVAAL 306 Query: 319 KERAQKNKVGNPFEQDTFQGPQVSQLQFDRIMEYINHGKKAGATVATGGDRHGN----EG 374 RA ++G+ + + GP VSQ ++ Y+ G GAT+ TGG R + +G Sbjct: 307 AARAATIRMGDGLDPASETGPLVSQDHLAKVEAYVALGISEGATLVTGGSRPTDPSLAKG 366 Query: 375 YFIQPTVFTDVTSDMKIAQEEIFGPVVTIQKFKDEAEAIKIGNSTDYGLAAAVHTKNVNT 434 F PT+ M+I QEE FGP++T+++F E EAI++GN T+YGLAA V T + Sbjct: 367 SFYLPTILDRCDRTMRIVQEETFGPILTVERFTTEEEAIRLGNDTEYGLAAGVRTSDPGR 426 Query: 435 AIRVSNALKAGTVWINNYNMISYQAPFGGFKQSGLGRELGSYALENYTQIKTV 487 RV+ AL+ GTVW+N++ + A +GGFK+SG GRELG L Y ++K + Sbjct: 427 GERVARALRHGTVWLNDFGYYTAAAEWGGFKKSGNGRELGPAGLAEYQELKHI 479 Lambda K H 0.318 0.134 0.397 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: 520 Number of extensions: 17 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: 497 Length of database: 494 Length adjustment: 34 Effective length of query: 463 Effective length of database: 460 Effective search space: 212980 Effective search space used: 212980 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 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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