Align Aldehyde dehydrogenase; EC 1.2.1.3 (characterized)
to candidate WP_051953139.1 DL86_RS09565 coniferyl aldehyde dehydrogenase
Query= SwissProt::P12693 (483 letters) >NCBI__GCF_000746085.1:WP_051953139.1 Length = 476 Score = 327 bits (837), Expect = 7e-94 Identities = 182/456 (39%), Positives = 267/456 (58%), Gaps = 17/456 (3%) Query: 35 GKFGIAERIAALNLLKETIQRREPEIIAALAADF-RKPASEVKLTEIFPVLQEINHAKRN 93 G + +R L LK + + +AA+ ADF + E L E+ PV++ I + RN Sbjct: 28 GPPSLKQRRGDLMRLKGALLAHREDFVAAINADFGHRSRQETSLLELSPVIEGIKYLHRN 87 Query: 94 LKDWMKPRRVRAALSVAGTRAGLRYEPKGVCLIIAPWNYPFNLSFGPLVSALAAGNSVVI 153 L WM+P R + + + Y+P GV +I+PWNYP L+ PL +ALAAGN V+I Sbjct: 88 LALWMRPERRKVSFHFFPGSTRVLYQPLGVVGVISPWNYPVALALMPLATALAAGNRVMI 147 Query: 154 KPSELTPHTATLIGSIVREAFSVDLVAVVEGDAAVSQELLALPFDHIFFTGSPRVGKLVM 213 KPSE+TP T+ L+ +++ E FS+D AV G+A V ALPFDH+ FTGS VG+ VM Sbjct: 148 KPSEITPATSALMSAVLGEIFSLDQAAVATGEADVGMAFAALPFDHLVFTGSTPVGRSVM 207 Query: 214 EAASKTLASVTLELGGKSPTIIGPTANLPKAARNIVWGKFSNNGQTCIAPDHVFVHRCIA 273 AAS L VTLELGGKSP I+ + L AR I +GK +N GQTCIAPD+V A Sbjct: 208 RAASDNLVPVTLELGGKSPVIVERGSCLKTTARRIAYGKLANGGQTCIAPDYVL---AAA 264 Query: 274 QKFNEIL---VKEIVRVYGKDFAAQRRSADYCRIVNDQHFNRINKLLTDAKAKGAKILQG 330 Q+ N+ + E+ ++Y D AA + DY I+ND H+ R+ LL DA+AKGA++++ Sbjct: 265 QEINDFVAAYAAEVEKLY-PDIAA---NPDYTSIINDHHYARLVGLLDDARAKGARVIEI 320 Query: 331 GQVD-----ATERLVVPTVLSNVTAAMDINHEEIFGPLLPIIEYDDIDSVIKRVNDGDKP 385 G R + P ++ T M++ EEIFGP+LP+I Y ++ + VN +P Sbjct: 321 GAAPKEGERTNARTLAPAIVLGATDGMNVMKEEIFGPILPVIPYARLEEAVAYVNARPRP 380 Query: 386 LALYVFSEDKQFVNNIVARTSSGSVGVNLSVVHFLHPNLPFGGVNNSGIGSAHGVYGFRA 445 LALY F D ++ART+SG V +N +++H+ ++PFGGV SG+G+ HG GF+ Sbjct: 381 LALYFFGPDGPGRRMVLARTTSGGVSINETILHYAQDDIPFGGVGASGMGAYHGHEGFKT 440 Query: 446 FSHEKPVLID-KFSITHWLFPPYTKKVKQLIGITVK 480 SH + V K ++T + PP+ K ++L+ ++ Sbjct: 441 LSHSRGVFEQAKVNLTDVVRPPFGKLFERLVDFLLR 476 Lambda K H 0.320 0.136 0.395 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: 534 Number of extensions: 21 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: 483 Length of database: 476 Length adjustment: 34 Effective length of query: 449 Effective length of database: 442 Effective search space: 198458 Effective search space used: 198458 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