Align Aldehyde dehydrogenase; EC 1.2.1.3 (characterized)
to candidate N515DRAFT_4224 N515DRAFT_4224 coniferyl-aldehyde dehydrogenase
Query= SwissProt::P12693 (483 letters) >FitnessBrowser__Dyella79:N515DRAFT_4224 Length = 456 Score = 331 bits (848), Expect = 4e-95 Identities = 192/444 (43%), Positives = 253/444 (56%), Gaps = 8/444 (1%) Query: 41 ERIAALNLLKETIQRREPEIIAALAADFR-KPASEVKLTEIFPVLQEINHAKRNLKDWMK 99 ER L L + I EI A+ DF +PA E L E+FP L I HA + + WMK Sbjct: 15 ERARRLRALNDLIGEHRGEIADAIHQDFGGRPAQETDLLEVFPSLSAIRHALAHGRRWMK 74 Query: 100 PRRVRAALSVAGTRAGLRYEPKGVCLIIAPWNYPFNLSFGPLVSALAAGNSVVIKPSELT 159 PRR L R +R +P GV II PWNYP L+ GP+V ALAAGN V++K SE T Sbjct: 75 PRRSWPGLLFMPARNEIRPQPLGVVGIIVPWNYPLFLAAGPMVDALAAGNRVMVKMSEYT 134 Query: 160 PHTATLIGSIVREAFSVDLVAVVEGDAAVSQELLALPFDHIFFTGSPRVGKLVMEAASKT 219 P + L + F + V VV GDA V+Q ALPFDH+ FTGS VG+ VM AAS Sbjct: 135 PQFSALFAQLAARYFKPEEVCVVTGDADVAQAFSALPFDHLLFTGSTAVGRHVMRAASAN 194 Query: 220 LASVTLELGGKSPTIIGPTANLPKAARNIVWGKFSNNGQTCIAPDHVFVHRCIAQKFNEI 279 L VTLELGGKSP I+GP A A I+ GK N GQTCIAPD+V + R +F Sbjct: 195 LTPVTLELGGKSPAIVGPGARFANAVERILVGKLFNAGQTCIAPDYVLLPRAQVDEFVAA 254 Query: 280 LVKEIVRVYGKDFAAQRRSADYCRIVNDQHFNRINKLLTDAKAKGAKI-LQGGQVDATE- 337 R+Y + R+ Y I++++ + R+ L DA GAK+ L G + D + Sbjct: 255 ARDVAARLYPQPV----RNEQYASIISERQYQRLAALRDDAARDGAKLTLLGDETDDIQR 310 Query: 338 RLVVPTVLSNVTAAMDINHEEIFGPLLPIIEYDDIDSVIKRVNDGDKPLALYVFSEDKQF 397 R + P +L+ V+ +M + EEIFGPLLP++ YDDI+ I V PLALY+F ED Sbjct: 311 RRMTPALLTGVSESMAVMQEEIFGPLLPLVPYDDIEQAIAYVAAHPHPLALYLFEEDGAL 370 Query: 398 VNNIVARTSSGSVGVNLSVVHFLHPNLPFGGVNNSGIGSAHGVYGFRAFSHEKPVLID-K 456 V+ ++ART++G V +N ++ H +LPFGGV SG G HG GFR FSH K V + Sbjct: 371 VDRVLARTTAGGVTINDTLYHIAQHDLPFGGVGPSGSGGYHGEAGFRTFSHLKSVFRQAR 430 Query: 457 FSITHWLFPPYTKKVKQLIGITVK 480 + L PPY ++ KQ++ I +K Sbjct: 431 VNGAGLLNPPYGQRFKQMLAIMLK 454 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: 484 Number of extensions: 16 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: 456 Length adjustment: 33 Effective length of query: 450 Effective length of database: 423 Effective search space: 190350 Effective search space used: 190350 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 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