Align aldehyde dehydrogenase ALDH; EC 1.2.1.3 (characterized)
to candidate WP_092345688.1 BLU87_RS05845 aldehyde dehydrogenase family protein
Query= CharProtDB::CH_007936 (497 letters) >NCBI__GCF_900107645.1:WP_092345688.1 Length = 477 Score = 300 bits (768), Expect = 7e-86 Identities = 181/475 (38%), Positives = 268/475 (56%), Gaps = 11/475 (2%) Query: 23 INNEFVKG--VEGKTFQV-INPSNEK-VITSVHEATEKDVDVAVAAARAAFEGPWRQVTP 78 +N ++ G VE + INPS+ +I A E+ + A+ AA+AA WR V Sbjct: 3 LNKNYINGEWVESNDVNLDINPSDTNDIIGEYARADEQQTNDAIQAAKAA-RNVWRDVCV 61 Query: 79 SERGILINKLADLMERDIDTLAAIESLDNGKAFTMAKVDLANSIGCLRYYAGWADKIHGQ 138 +E+ I+++ + + LA + + + GK A ++ + ++++G A ++ G Sbjct: 62 NEKSIILDNIGSEILARKTELATLLAREEGKTLPEATGEVVRAGMIFKFFSGEAVRLTGD 121 Query: 139 TI-DTNPETLTYTRHEPVGVCGQIIPWNFPLLMWSWKIGPAVAAGNTVVLKTAEQTPLSA 197 + T P EPVGV G I PWNFP+ + +WKI PA+A GNTVVLK+A+ P SA Sbjct: 122 ILASTRPGLNVEITREPVGVIGVISPWNFPIAIPAWKIAPALAFGNTVVLKSADLVPASA 181 Query: 198 LYAAKLIKEAGFPAGVINVISGFGRTAGAAISSHMDIDKVAFTGSTLVGRTILQAAAKSN 257 A++I AG PAG N++ G G G I + DID V FTGS +G I A Sbjct: 182 WALAEIISRAGLPAGAFNLVMGSGSKVGDTIVNSPDIDAVTFTGSDAIGNGIRGKVAGRG 241 Query: 258 LKKVTLELGGKSPNIVFDDADIDNAISWANFGIFFNHGQCCCAGSRILVQEGIYDKFVAR 317 KV LE+GGK+P +V DDAD+D AI+ A G FF GQ C A SR++V EGI+D FVA Sbjct: 242 -AKVQLEMGGKNPLVVLDDADLDTAINAAVDGAFFGTGQRCTASSRLIVTEGIHDAFVAG 300 Query: 318 FKERAQKNKVGNPFEQDTFQGPQVSQLQFDRIMEYINHGKKAGATVATGGD--RHGNEGY 375 ER Q + G+ + + GP SQ Q +EYI+ GK+ GA +A GG+ + GY Sbjct: 301 VIERLQGLRTGHALDSKSQIGPVSSQAQLQTDLEYISIGKEEGAHLAYGGELLQRDTPGY 360 Query: 376 FIQPTVFTDVTSDMKIAQEEIFGPVVTIQKFKDEAEAIKIGNSTDYGLAAAVHTKNVNTA 435 ++ P +FT+ +DM++ +EE+FGPV T+ + K+ EA+++ N T +GL + + T ++ ++ Sbjct: 361 YLSPALFTETDNDMRLNREEVFGPVATVIRAKNYEEALELANDTRFGLTSGICTTSLESS 420 Query: 436 IRVSNALKAGTVWINNYNM-ISYQAPFGGFKQSGLG-RELGSYALENYTQIKTVH 488 +AG V +N I Y PFGG K S G RE GSYA E +T +KT + Sbjct: 421 KDFKRNSEAGMVMVNLPTAGIDYHVPFGGRKNSSYGSREQGSYAREFFTIVKTCY 475 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: 517 Number of extensions: 27 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: 497 Length of database: 477 Length adjustment: 34 Effective length of query: 463 Effective length of database: 443 Effective search space: 205109 Effective search space used: 205109 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