Align Putative aldehyde dehydrogenase YwdH; EC 1.2.1.3 (uncharacterized)
to candidate Synpcc7942_0489 Synpcc7942_0489 aldehyde dehydrogenase
Query= curated2:P39616 (456 letters) >FitnessBrowser__SynE:Synpcc7942_0489 Length = 459 Score = 425 bits (1093), Expect = e-123 Identities = 215/443 (48%), Positives = 289/443 (65%) Query: 12 KAYFAAGHTRPLESRLNILRKLKQAVRTHEADLIAALYQDLHKSEQEAYSTEIGIVLEEI 71 +A F G TR L RL L+ L + V +EA+L+ AL DL K EAY++EI V ++I Sbjct: 17 QATFDRGDTRTLAFRLARLQDLAKLVADNEAELLQALASDLRKPALEAYASEIYFVRDQI 76 Query: 72 SFVMKRLRKWSKPKRVKTPLTHLGSKSIIIPEPYGTVLVIAPWNYPLQLALSPLIGAIAA 131 K LR+W +P++ L ++ EP G VL+I PWNYP QL ++PLIGAIAA Sbjct: 77 KLTCKHLRRWMQPEKQSISLMQQPGQAYRQAEPLGVVLIIGPWNYPFQLLITPLIGAIAA 136 Query: 132 GNTVVLKPSEYTPAVSAILSKLISSVFPTDYVAMAEGGPDVSTALLQQPFDYIFFTGSVA 191 GN VLKPSE PA S+++ +LIS F DY+ + EG VS AL+ QPFD+IFFTG A Sbjct: 137 GNCAVLKPSELAPATSSLIQRLISDRFDPDYIRVLEGDASVSQALITQPFDHIFFTGGTA 196 Query: 192 VGKIVMEAAAKQLIPVTLELGGKSPCIVHKDADIQLAAKRIVFGKFTNAGQTCIAPDYLF 251 +G+ VM AAA+ L PVTLELGGKSPCIV D D+ +AA+RI +GKF NAGQTCIAPDYL Sbjct: 197 IGRKVMAAAAENLTPVTLELGGKSPCIVDTDIDLDVAARRIAWGKFFNAGQTCIAPDYLL 256 Query: 252 VHEDIKTKLTEEMKRAIREFYGPQPERNPQYGKIVSERHYQRLLSFLNDGIPLTGGQSDP 311 V + E + I++FYG P+++ Y +IVS+RH+QRL S L DG GGQ D Sbjct: 257 VQRTVAEPFIEALIDNIQQFYGEDPQQSADYARIVSDRHWQRLNSLLVDGTIRHGGQVDR 316 Query: 312 NHHKIAPTILEQVRDDSPVMQEEIFGPILPLFTYRNIGEVIEKVQSRPKPLALYLFTTNK 371 + IAPT++ V P++QEEIFGP+LP+ Y + E I +++++PKPLALYLF+ ++ Sbjct: 317 SDRYIAPTLITDVNWRDPILQEEIFGPLLPILIYDQLDEAIAQIRAQPKPLALYLFSRDR 376 Query: 372 EIERAVLGNLSFGGGCVNDTLMHVATPYLPFGGVGESGIGSYHGFDSFNTFTHKKSVVKQ 431 +++ VL S G C+NDT++ V P FGGVG SG+G YHG SF TF+H K V+K+ Sbjct: 377 QVQERVLAETSAGSVCLNDTILQVGVPDAAFGGVGPSGMGGYHGKASFETFSHYKLVLKR 436 Query: 432 TNRFDFAFRYPSSKNGLRMIRKI 454 D A RYP + + + RK+ Sbjct: 437 PFWLDLALRYPPYGDKINLFRKL 459 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: 565 Number of extensions: 13 Number of successful extensions: 1 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 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