Align Alpha-aminoadipic semialdehyde dehydrogenase; Alpha-AASA dehydrogenase; Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Betaine aldehyde dehydrogenase; Delta1-piperideine-6-carboxylate dehydrogenase; P6c dehydrogenase; EC 1.2.1.31; EC 1.2.1.3; EC 1.2.1.8 (characterized)
to candidate PP_3646 PP_3646 Aldehyde dehydrogenase family protein
Query= SwissProt::Q64057 (539 letters) >FitnessBrowser__Putida:PP_3646 Length = 493 Score = 219 bits (557), Expect = 2e-61 Identities = 154/480 (32%), Positives = 234/480 (48%), Gaps = 12/480 (2%) Query: 56 NGSW--GGRGEVITTYCPANNEPIARVRQASMKDYEETIGKAKKAWN--IWADIPAPKRG 111 +G W G+ + PA + A++ A D E + A++A++ W I A RG Sbjct: 11 DGQWRDAQSGKTFDSLNPATAQAWAQLPDADEADVELAVQAAQRAFDSKAWRSITATARG 70 Query: 112 EIVRKIGDALREKIQLLGRLVSLEMGKILVEGIGEVQEYVDVCDYAAGLSRMIGGPTLPS 171 +++R++GD + E + L +L S + GK++ E G+V + Y AGL+ + G TLP Sbjct: 71 KLLRRLGDLIAENKEHLAQLESRDNGKLIRETRGQVGYLPEFFHYTAGLADKLEGGTLPL 130 Query: 172 ERPGHALMEQWNPLGLVGIITAFNFPVAVFGWNNAIALITGNVCLWKGAPTTSLVSIAVT 231 ++P P+G+V I +N P+ + A AL GN + K + S + + Sbjct: 131 DKPDLFAYTVHEPIGVVAGIIPWNSPLYLTAIKLAPALAAGNTIVLKPSEHASATILELA 190 Query: 232 KIIAKVLEDNLLPGAICSLTCGGADMGTAMARDERVNLLSFTGSTQVGKQVALMVQERFG 291 ++ LE G + +T G G A+ R V ++FTG + V E F Sbjct: 191 RL---ALEAGFPAGVVNVVTGYGPSTGAALTRHPLVRKIAFTGGAATARHVVRSSAENFA 247 Query: 292 KSLLELGGNNAIIAFEDADLSLVLPSALFAAVGTAGQRCTTVRRLFLHESIHDEVVDRLK 351 K LELGG + I F DADL + A+ +GQ C RL + + I DE V+RL Sbjct: 248 KLSLELGGKSPNIIFADADLDSAINGAVAGIYAASGQSCVAGSRLLVQDEIFDEFVERLI 307 Query: 352 NAYSQIRVGNPWDPNILYGPLHTKQAVSMFVQAVEEAKKEGGTVVYGGKVMDHPGN--YV 409 +IR+GNP D GP+ T Q +++ V AK EG + GGK D G+ + Sbjct: 308 ARAKRIRIGNPQDDASEMGPMATAQQLAVVEGLVAAAKAEGAKLHMGGKRADVEGDGWFY 367 Query: 410 EPTIVTGLVHDAPIVHKETFAPILYVFKFKNEEEVFEWNNEVKQGLSSSIFTKDLGRIFR 469 EPT+ + I+ +E F P+ V +FK EEE N+ + GL++ I+T+DLGR R Sbjct: 368 EPTLFECDSNAMTIMQEEVFGPVAAVIRFKTEEEALAMANDSQFGLAAGIWTRDLGRAHR 427 Query: 470 WLGPKGSDCGIVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQYMRRSTCTINYSTA 529 S GI+ VN + + + GG K++G GRESG D+ Y T IN STA Sbjct: 428 LARDVRS--GIIWVNTYRAVSAM-APIGGFKNSGYGRESGIDSVLAYTELKTVWINLSTA 484 Lambda K H 0.319 0.137 0.417 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: 628 Number of extensions: 31 Number of successful extensions: 4 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: 539 Length of database: 493 Length adjustment: 35 Effective length of query: 504 Effective length of database: 458 Effective search space: 230832 Effective search space used: 230832 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 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