Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate Ac3H11_1496 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= metacyc::MONOMER-16244 (495 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1496 Length = 500 Score = 384 bits (987), Expect = e-111 Identities = 200/479 (41%), Positives = 292/479 (60%), Gaps = 8/479 (1%) Query: 18 EQPTGLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSS-WS 76 E+ G I + S + P+TE + + ++ + DI AV +A AF S W Sbjct: 19 ERRVGNVIGGVSGPALSGRWLPVTDPATEMVVAEAPDSDAADIARAVASAQRAFDSHVWR 78 Query: 77 TSDPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKG-DVALTAAYFRSCAGWTD 135 P R K+L++L++LI+ HAD L+ +E L +GK ++ DV A + R AGW Sbjct: 79 GLRPADREKLLFRLSELIERHADELSALETLQSGKLQGIARAIDVQAGAEFVRYMAGWAT 138 Query: 136 KIKGSVIET-----GDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLK 190 K++G ++ G YTRREP+GV G I+PWNFPL +A WK+ P L GCT VLK Sbjct: 139 KLEGQTLDNSIPIPGPQWVTYTRREPVGVVGAIVPWNFPLAIALWKIAPALAAGCTVVLK 198 Query: 191 TAESTPLSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRH 250 +E TPL+AL LA L EAG P GV+NVV G G TAGA + +HP ++K++FTGSTA G+ Sbjct: 199 PSEDTPLTALRLAHLALEAGIPEGVLNVVCGRGATAGAALIAHPGVRKLSFTGSTAVGKV 258 Query: 251 IMKAAAESNLKKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQE 310 + AA E N+ + TLELGGKSP +V +DAD Q + TGIF++ G+VC A SR+ V Sbjct: 259 VGHAAVE-NMARFTLELGGKSPAVVMEDADPSQVAQGIATGIFFHQGQVCTASSRLLVHR 317 Query: 311 GIYDKIVSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGE 370 +Y +++ E A+ ++IG F T G TS+ +++ +I K EGAT++ GGE Sbjct: 318 SLYRRVLDELAGIAQGMRIGSGFDAATQFGPLTSKAHFARVMDFIASAKAEGATLVAGGE 377 Query: 371 RFGNKGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVH 430 R + G F++PTIF D ++VR+E+FGPV+ + F VE+ IA AND+ YGLAA + Sbjct: 378 RVHDAGCFVQPTIFADTTAQMRVVREEVFGPVLAVAPFDDVEDAIAAANDTPYGLAASLW 437 Query: 431 TTNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAV 489 T +LS A + ++ +G +WVN +N +P GG QSG GR++G A++ +T++K+V Sbjct: 438 TQSLSHAHRIVPRLQAGVVWVNAHNVLDAGLPLGGIKQSGTGRDLGRAAVEGFTELKSV 496 Lambda K H 0.316 0.133 0.389 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: 527 Number of extensions: 18 Number of successful extensions: 3 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: 495 Length of database: 500 Length adjustment: 34 Effective length of query: 461 Effective length of database: 466 Effective search space: 214826 Effective search space used: 214826 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 (21.6 bits) S2: 52 (24.6 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