Align Aldehyde dehydrogenase; EC 1.2.1.3 (characterized)
to candidate WP_041099790.1 SUTH_RS13010 coniferyl aldehyde dehydrogenase
Query= SwissProt::P12693 (483 letters) >NCBI__GCF_000828635.1:WP_041099790.1 Length = 473 Score = 320 bits (821), Expect = 5e-92 Identities = 183/456 (40%), Positives = 255/456 (55%), Gaps = 8/456 (1%) Query: 29 ASSARRGKFGIAERIAALNLLKETIQRREPEIIAALAADF-RKPASEVKLTEIFPVLQEI 87 A++ R + + R A L+ L + + A++ADF + A E +L E+FP L+ I Sbjct: 22 AATRRNAQVERSARKARLDALVALVHDNAERFVTAISADFGHRSAHETRLLELFPSLESI 81 Query: 88 NHAKRNLKDWMKPRRVRAALSVAGTRAGLRYEPKGVCLIIAPWNYPFNLSFGPLVSALAA 147 H + + WMKP+R A++ RA + +P GV II PWNYP L+ PL +ALAA Sbjct: 82 RHTRSHFGGWMKPQRKSASIWFRPGRARIIPQPLGVVGIIVPWNYPLFLAVSPLAAALAA 141 Query: 148 GNSVVIKPSELTPHTATLIGSIVREAFSVDLVAVVEGDAAVSQELLALPFDHIFFTGSPR 207 GN V+IK SE TP T L+ + + F+ D V+VV GDA V + LPFDH+ FTGS + Sbjct: 142 GNRVMIKMSEFTPRTGELLAELAAKYFAADDVSVVLGDATVGADFARLPFDHLLFTGSTK 201 Query: 208 VGKLVMEAASKTLASVTLELGGKSPTIIGPTANLPKAARNIVWGKFSNNGQTCIAPDHVF 267 VG +M A+ L VTLELGGKSP I+GP + KAA I+ GK N GQTCIAPD+V Sbjct: 202 VGHDIMRMAADNLTPVTLELGGKSPAIVGPDYPMAKAAERIMIGKLLNAGQTCIAPDYVL 261 Query: 268 VHRCIAQKFNEILVKEIVRVYGKDFAAQRRSADYCRIVNDQHFNRINKLLTDAKAKGAKI 327 V Q F + V K F A + DY IVND+H+ R+ + DA+A+GAK+ Sbjct: 262 VPAGQEQAF----IDAARAVVAKCFPALASTPDYTAIVNDRHYQRLQGYVADAEARGAKV 317 Query: 328 --LQGGQVDATERLVVPTVLSNVTAAMDINHEEIFGPLLPIIEYDDIDSVIKRVNDGDKP 385 L D R + P L NV M + +EIFGPLLP++ Y ++D+ I VN +P Sbjct: 318 EPLSTTMPDDARRRLPPLALLNVDDDMRVMQDEIFGPLLPVLPYANLDAAISYVNQHPRP 377 Query: 386 LALYVFSEDKQFVNNIVARTSSGSVGVNLSVVHFLHPNLPFGGVNNSGIGSAHGVYGFRA 445 LALY F D + ++ T +G V +N +++H LPFGGV SG+G HG GF+ Sbjct: 378 LALYCFENDTGRRDRVLNETVAGGVTINDTILHIAQEELPFGGVGPSGMGHYHGYEGFKT 437 Query: 446 FSHEKPVLIDKFSITHWLF-PPYTKKVKQLIGITVK 480 F+ +K V + LF PPY ++L ++ Sbjct: 438 FTKQKAVFYQSWLNGMSLFNPPYGALFERLTKFLIR 473 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: 521 Number of extensions: 30 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: 483 Length of database: 473 Length adjustment: 34 Effective length of query: 449 Effective length of database: 439 Effective search space: 197111 Effective search space used: 197111 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 Apr 09 2024. 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