Align Aldehyde dehydrogenase; EC 1.2.1.3 (characterized)
to candidate Echvi_1497 Echvi_1497 NAD-dependent aldehyde dehydrogenases
Query= SwissProt::P12693 (483 letters) >FitnessBrowser__Cola:Echvi_1497 Length = 469 Score = 400 bits (1029), Expect = e-116 Identities = 213/446 (47%), Positives = 289/446 (64%), Gaps = 2/446 (0%) Query: 39 IAERIAALNLLKETIQRREPEIIAALAADFRKPASEVKLTEIFPVLQEINHAKRNLKDWM 98 ++ RI L LKE I+ + EI AL AD RKPA+EV +TE V+ EIN A + L W Sbjct: 21 LSSRIKKLEQLKEWIKSNQKEIEKALYADLRKPAAEVAVTETSFVVMEINAALKQLPKWT 80 Query: 99 KPRRVRAALSVAGTRAGLRYEPKGVCLIIAPWNYPFNLSFGPLVSALAAGNSVVIKPSEL 158 P +V + + GT+A L+ EPKG LII+PWNYPFNLS PLVSA+AAG S +KPSE Sbjct: 81 APTKVGQPIHMLGTQAYLQAEPKGAVLIISPWNYPFNLSVAPLVSAIAAGCSACLKPSEH 140 Query: 159 TPHTATLIGSIVREAFSVDLVAVVEGDAAVSQELLALPFDHIFFTGSPRVGKLVMEAASK 218 +PHT+ L+ +V E F+V+ V + EG V+ ELL PFDHIFFTGS VGK+VM+AA+K Sbjct: 141 SPHTSALLRRMVTELFAVEDVTIFEGGVPVTSELLEQPFDHIFFTGSTEVGKIVMKAAAK 200 Query: 219 TLASVTLELGGKSPTIIGPTANLPKAARNIVWGKFSNNGQTCIAPDHVFVHRCIAQKFNE 278 L SVTLELGGKSP II +L AA+ I GKF N+GQTCIAPD++FVH Q F E Sbjct: 201 NLTSVTLELGGKSPAIIDQGFDLEDAAKKIAIGKFINSGQTCIAPDYLFVHESQKQDFIE 260 Query: 279 ILVKEIVRVYGKDFAAQRRSADYCRIVNDQHFNRINKLLTDAKAKGAKILQGGQVDATER 338 L ++ R+Y + R+ DY RI++ H R+ +L DA+ KGA + GG+ ++ Sbjct: 261 TLKAQVNRMYNANGKGFDRNPDYGRIIHAPHIVRLQNMLKDAQTKGAHVEFGGKNSLDQQ 320 Query: 339 LVVPTVLSNVTAAMDINHEEIFGPLLPIIEYDDIDSVIKRVNDGDKPLALYVFSEDKQFV 398 + PTV+SNV+ AMD+ EEIFGP+LPII Y +D VI+ + KPLA+Y F+ D + + Sbjct: 321 FMEPTVVSNVSEAMDLMKEEIFGPILPIITYHQLDDVIQLIQLKPKPLAVYAFTTDDRII 380 Query: 399 NNIVARTSSGSVGVNLSVVHFLHPNLPFGGVNNSGIGSAHGVYGFRAFSHEKPVLIDKF- 457 + TSSG++ +N + FLH LPFGG+ SG+G +HG GF AFS+EK +L + Sbjct: 381 EQLSKNTSSGALVINDCAIQFLHSELPFGGIGASGMGRSHGHAGFLAFSNEKAILKQRTG 440 Query: 458 -SITHWLFPPYTKKVKQLIGITVKYL 482 ++ L+PPY K +I +K++ Sbjct: 441 KTLPKLLYPPYGLKTSGIIKAFMKWV 466 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: 506 Number of extensions: 20 Number of successful extensions: 1 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: 469 Length adjustment: 33 Effective length of query: 450 Effective length of database: 436 Effective search space: 196200 Effective search space used: 196200 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