Align Putative aldehyde dehydrogenase YwdH; EC 1.2.1.3 (uncharacterized)
to candidate WP_075617353.1 GY23_RS01060 aldehyde dehydrogenase
Query= curated2:P39616 (456 letters) >NCBI__GCF_001939075.1:WP_075617353.1 Length = 462 Score = 436 bits (1122), Expect = e-127 Identities = 211/455 (46%), Positives = 306/455 (67%), Gaps = 2/455 (0%) Query: 4 IPSIISKHKAYFAAGHTRPLESRLNILRKLKQAVRTHEADLIAALYQDLHKSEQEAYSTE 63 + +I++ +F G TR E R LR LKQA++ HE +++ ALY DLHKSE EAY+TE Sbjct: 8 VEHMITQQHDFFYTGATRSAEFRKQQLRNLKQAIQHHEREILQALYDDLHKSEFEAYATE 67 Query: 64 IGIVLEEISFVMKRLRKWSKPKRVKTPLTHLGSKSIIIPEPYGTVLVIAPWNYPLQLALS 123 IG VL+ I F++K L +W KP+ VKT L + +KS I+ EPYG+ L++ P+NYP QL + Sbjct: 68 IGFVLDSIGFMIKNLDEWMKPEPVKTSLHLMPAKSFIVREPYGSALIVGPFNYPFQLVME 127 Query: 124 PLIGAIAAGNTVVLKPSEYTPAVSAILSKLISSVFPTDYVAMAEGGPDVSTALLQQPFDY 183 PLIGAI GN ++KPSE +AI+ K+I S F +YV + EG + ++ L+ PFD Sbjct: 128 PLIGAIIGGNCAIVKPSESAVHTAAIIRKIIESTFTPNYVRVVEGEREETSILIHAPFDT 187 Query: 184 IFFTGSVAVGKIVMEAAAKQLIPVTLELGGKSPCIVHKDADIQLAAKRIVFGKFTNAGQT 243 IFFTGSVAVGK+VM+AAA++L PVTLELGGKSP I+ A++ +AAKRI +GKF NAGQT Sbjct: 188 IFFTGSVAVGKVVMKAAAERLTPVTLELGGKSPAIIDHTANLAVAAKRIAWGKFVNAGQT 247 Query: 244 CIAPDYLFVHEDIKTKLTEEMKRAIREFYGPQPERNPQYGKIVSERHYQRLLSFLNDGIP 303 C+APDYL V + +K + + +AI++FYG + +P YG+I++ + + RL + Sbjct: 248 CVAPDYLLVQQTVKDEFIHLLMQAIQDFYGEDVQASPDYGRIINAKQFDRLRQLIKQEGQ 307 Query: 304 --LTGGQSDPNHHKIAPTILEQVRDDSPVMQEEIFGPILPLFTYRNIGEVIEKVQSRPKP 361 + GG D + I PTI++ V +SP M++EIFGP+LP+ +Y + I +V+ PKP Sbjct: 308 HIIAGGNLDADDLYIEPTIIDGVSWNSPSMEDEIFGPLLPVISYDRLETAISQVRKLPKP 367 Query: 362 LALYLFTTNKEIERAVLGNLSFGGGCVNDTLMHVATPYLPFGGVGESGIGSYHGFDSFNT 421 L+ YLF+ N + L L FGGGC+NDT+ HV + ++PFGGVG SG+ +YHG SF Sbjct: 368 LSAYLFSENDKAIEYFLEQLPFGGGCINDTISHVGSSHMPFGGVGSSGMNAYHGKYSFEA 427 Query: 422 FTHKKSVVKQTNRFDFAFRYPSSKNGLRMIRKILK 456 FTH KS++K++ +F +P KN +++++ L+ Sbjct: 428 FTHAKSILKKSTKFSVNVAFPPYKNKVKLVKSFLR 462 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: 575 Number of extensions: 19 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: 462 Length adjustment: 33 Effective length of query: 423 Effective length of database: 429 Effective search space: 181467 Effective search space used: 181467 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