Align Putative aldehyde dehydrogenase AldY; EC 1.2.1.3 (characterized)
to candidate WP_012468985.1 GLOV_RS04485 aldehyde dehydrogenase
Query= SwissProt::P94358 (485 letters) >NCBI__GCF_000020385.1:WP_012468985.1 Length = 483 Score = 318 bits (814), Expect = 3e-91 Identities = 179/479 (37%), Positives = 271/479 (56%), Gaps = 6/479 (1%) Query: 10 FINGKWTGGESGRTEDILNPYDQSVITTASLATGKQLEDAFDIAQKAQKEWAKSTTEDRK 69 +ING W G D NPY ++TT + + + A + A A +WA ++ Sbjct: 8 YINGTWQDSADGSWFDDFNPYTGEILTTVANGSQQDALLAVNAAADAFPDWAAVAPSQKR 67 Query: 70 AVLQKARGYLHENRDDIIMMIARETGGTIIKSTIELEQTIAILDEAMTYTGELGGVKEVP 129 + KA L + +D++I ++ARETG + + L EA + + G +P Sbjct: 68 LLFLKAADLLEKRKDELIDLLARETGAARPFAAYQAAAGPNYLREAGSQAHRVTGTI-LP 126 Query: 130 SDIEGKTNKIYRLPLGVISSISPFNFPMNLSMRSIAPAIALGNSVVHKPDIQTAISGGTI 189 S+ K + + R P+GV++ ISP+N P+ LS+R++ A+A GN+VV KP ++ +SGG + Sbjct: 127 SETT-KVSMVMRHPVGVVAGISPWNCPVVLSLRAVCFAMAYGNTVVLKPSEESPVSGGIL 185 Query: 190 IAKAFEHAGLPAGVLNVMLTDV---KEIGDGMLTNPIPRLISFTGSTAVGRHIGEIAGRA 246 +A+ FE AG P GV N++ E+GD + + + ISFTGST VGR + E GR Sbjct: 186 LAELFEEAGFPKGVFNIVTHGYGRSSEVGDLFIQDRRVKRISFTGSTRVGRELAEKCGRH 245 Query: 247 FKRMALELGGNNPFAVLSDADVDRAVDAAIFGKFIHQGQICMIINRIIVHQDVYDEFVEK 306 KR+ALELGGN+P VL+DAD+D AV+AAIFG+F+HQGQ+CM R+I+ + V EF + Sbjct: 246 LKRIALELGGNDPLIVLNDADMDHAVNAAIFGRFLHQGQVCMNAKRLIIEKTVAQEFTAR 305 Query: 307 FTARVKQLPYGDQTDPKTVVGPLINERQIEKALEIIEQAKTDGIELAVEGKRVGNVLTPY 366 F AR L G+ D TV+GPLIN +Q E + +A +G EL G G P Sbjct: 306 FVARTSALKVGNPLDAATVIGPLINHKQYETLEGQVNRAVAEGAELLCGGYGNGLCYHPT 365 Query: 367 VFVGADNNSKIAQTELFAPIATIIKAGSDQEAIDMANDTEYGLSSAVFTSDLEKGEKFAL 426 V + I E F P+A II A +A+ +AN + YGLS+ + T+++++G A Sbjct: 366 VLGNVREDMSIFHEETFGPVAPIIVAEDADDALRLANSSAYGLSAGILTNNMQQGLALAR 425 Query: 427 QIDSGMTHVNDQSVNDSPNIAFGGNKASGVGRFGNPWVVEEFTVTKWISIQKQYRKYPF 485 +I+SG HVND + + GG SG G+FG + EFT +W++++ + R+YPF Sbjct: 426 RIESGACHVNDSPLYGETHAPLGGVNNSGWGKFGIE-AMHEFTEQQWVTLEMETRQYPF 483 Lambda K H 0.316 0.134 0.380 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: 601 Number of extensions: 27 Number of successful extensions: 4 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: 485 Length of database: 483 Length adjustment: 34 Effective length of query: 451 Effective length of database: 449 Effective search space: 202499 Effective search space used: 202499 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 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