Align Probable aldehyde dehydrogenase; EC 1.2.1.3 (uncharacterized)
to candidate WP_068863379.1 I603_RS06550 aldehyde dehydrogenase family protein
Query= curated2:P33008 (488 letters) >NCBI__GCF_001677335.1:WP_068863379.1 Length = 475 Score = 376 bits (966), Expect = e-109 Identities = 204/466 (43%), Positives = 288/466 (61%), Gaps = 11/466 (2%) Query: 29 IGGHGVATSDYLPVLNPATRQPIGQCPVASEEHVEQARAAAGDAFAVWRQVPYGKRCEQL 88 IGG +AT +L V+NPAT Q IGQ P ++ +++A AAA AF W++ P +R + Sbjct: 9 IGGEMIATDRWLDVVNPATEQVIGQVPACGKDELDKAVAAARAAFKTWKKTPIEERRAAI 68 Query: 89 QALAGILEAHLDELAQLLTHEQGKPLADARGELAGAIAFCQCAGSLPLPEVVHEQSATRL 148 A++G ++ + +EL +LLT EQGKP A+GE+ GA +L L + ++E S RL Sbjct: 69 MAISGAIKENAEELYRLLTSEQGKPHDQAKGEIYGAAGMSAAQSTLSLDDEINEDSDARL 128 Query: 149 SKTVREPLGVVVAIVPWNYPVSIAFVK--PDRRVGCRKHADSQAGADHAADYLRIGELIR 206 S+T R P+GVV IVPWN+PV +A K P GC LRI ELI Sbjct: 129 SRTRRVPVGVVGGIVPWNFPVMMAIQKIVPAMLSGCTIVLKPSPFTPLTT--LRIAELIA 186 Query: 207 DALPAGVINVLAGNDDLGPWLTGHADVAKISFTGSSVTGRHVARSAAADLKRLTLELGGN 266 D +PAGV+N++ G DDLGP +T H D+ KI+FTGS+ TG+ + A+ADLKR+TLELGGN Sbjct: 187 DKVPAGVVNIITGEDDLGPMITSHPDIDKITFTGSTATGKKIMEGASADLKRITLELGGN 246 Query: 267 DAAVVMADSLSDAVVERVFWSAFTNAGQICMATKRLYIHESIYEAFRDKLVAYAQNVVIG 326 DA++V+ D+ V E++FWS+F+NAGQIC+A KR+YIHE IY+ +V YA+ V +G Sbjct: 247 DASIVLPDADPKKVAEQLFWSSFSNAGQICVAAKRVYIHEDIYDELSAAIVEYAKTVKVG 306 Query: 327 DGSQPGVTMGPLQNAKQFAKVMSLIDAVRQRGGRLIECGQM-RGGDGYFLPITFVDLPDE 385 DGSQ G +GP+QN KQ+ +V+ LI+ + G + + G G GYF+P+T +D P E Sbjct: 307 DGSQQGTGVGPIQNKKQYDRVLELIEDAKSNGYKFLLGGNADPSGTGYFVPLTILDNPPE 366 Query: 386 SAPEVVEEAFGPLLPLLKFRDVDEVIERVNAARTGWLAASGVVIGRSAHGL---QQPSTR 442 A V EE FGP++PL+KF +EVI R N + G A V G+ +Q T Sbjct: 367 DARIVAEEQFGPVMPLMKFSSEEEVIARANNSEYG--LAGAVWTANPEKGVEIAEQLETG 424 Query: 443 SVWSTTGCDHAVYS-FGGMKASGYGAESGLEGLLEFTTQKTVIIQQ 487 +VW + ++ FGG K SG+GAE G EGL EFT + + +++ Sbjct: 425 TVWVNEYLHLSPFAPFGGHKQSGFGAEYGKEGLKEFTYPQVITVKK 470 Lambda K H 0.319 0.134 0.398 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: 590 Number of extensions: 26 Number of successful extensions: 5 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: 488 Length of database: 475 Length adjustment: 34 Effective length of query: 454 Effective length of database: 441 Effective search space: 200214 Effective search space used: 200214 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 (21.7 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