Align Putative aldehyde dehydrogenase YwdH; EC 1.2.1.3 (uncharacterized)
to candidate WP_011612208.1 TERY_RS12690 aldehyde dehydrogenase
Query= curated2:P39616 (456 letters) >NCBI__GCF_000014265.1:WP_011612208.1 Length = 459 Score = 439 bits (1129), Expect = e-128 Identities = 218/454 (48%), Positives = 305/454 (67%), Gaps = 2/454 (0%) Query: 2 NSIPSIISKHKAYFAAGHTRPLESRLNILRKLKQAVRTHEADLIAALYQDLHKSEQEAYS 61 +SI ++++K + +FA G T+ ++ R+ L+ LKQAV ++ ++AA+ DL+++E EAY Sbjct: 6 SSISNLLNKQRKFFATGKTKNIDFRIEQLKGLKQAVSDYQNKIVAAVKADLNRAEFEAYF 65 Query: 62 TEIGIVLEEISFVMKRLRKWSKPKRVKTPLTHLGSKSIIIPEPYGTVLVIAPWNYPLQLA 121 EI+ +K+L+ W+KP+RV TP+ + + I EP G VL+I WNYP QL Sbjct: 66 ELT--FFPEINDGIKKLKSWAKPRRVSTPIEQFPAGAKIYQEPLGVVLIIGAWNYPFQLV 123 Query: 122 LSPLIGAIAAGNTVVLKPSEYTPAVSAILSKLISSVFPTDYVAMAEGGPDVSTALLQQPF 181 + PL+GAIAAGN ++KPSE S +++ LI+ F + Y+A GG + S LL + F Sbjct: 124 IHPLLGAIAAGNCAIIKPSEIAVNTSEVVADLIAHTFDSSYIAAVTGGVEKSQQLLAEKF 183 Query: 182 DYIFFTGSVAVGKIVMEAAAKQLIPVTLELGGKSPCIVHKDADIQLAAKRIVFGKFTNAG 241 D+IFFTG VGKIVMEAAAK L PVTLELGGKSPCIV D ++ AKRI +GKF NAG Sbjct: 184 DHIFFTGGTRVGKIVMEAAAKSLTPVTLELGGKSPCIVDDDIQLEYTAKRITWGKFINAG 243 Query: 242 QTCIAPDYLFVHEDIKTKLTEEMKRAIREFYGPQPERNPQYGKIVSERHYQRLLSFLNDG 301 QTC+APDYL V++ +K+ L E++K++I +FYG P +P YG+I++E+ + RL L +G Sbjct: 244 QTCVAPDYLLVNKSVKSDLLEKIKQSIDKFYGKNPANSPDYGRIINEKQFNRLNHLLEEG 303 Query: 302 IPLTGGQSDPNHHKIAPTILEQVRDDSPVMQEEIFGPILPLFTYRNIGEVIEKVQSRPKP 361 GG++ I+PT++E V DS +M+EEIFGPILP+ Y N+ E I V SRPKP Sbjct: 304 KIFIGGETKSEELYISPTVIEGVNWDSGIMEEEIFGPILPVLEYENLDEAIALVNSRPKP 363 Query: 362 LALYLFTTNKEIERAVLGNLSFGGGCVNDTLMHVATPYLPFGGVGESGIGSYHGFDSFNT 421 L+LY F+ NK+ + VL S G C+NDT+M +LPFGGVG SGIGSYHG SF+T Sbjct: 364 LSLYFFSRNKQKQEQVLRETSSGNVCINDTVMQFVVRFLPFGGVGNSGIGSYHGKASFDT 423 Query: 422 FTHKKSVVKQTNRFDFAFRYPSSKNGLRMIRKIL 455 F+H KSV+ + FD FRY KN + +I+KI+ Sbjct: 424 FSHYKSVLNKGLWFDLKFRYAPYKNKVGLIKKII 457 Lambda K H 0.320 0.137 0.401 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: 616 Number of extensions: 23 Number of successful extensions: 2 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: 456 Length of database: 459 Length adjustment: 33 Effective length of query: 423 Effective length of database: 426 Effective search space: 180198 Effective search space used: 180198 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: 51 (24.3 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