Align aldehyde dehydrogenase ALDH; EC 1.2.1.3 (characterized)
to candidate CA265_RS24850 CA265_RS24850 aldehyde dehydrogenase
Query= CharProtDB::CH_007936 (497 letters) >FitnessBrowser__Pedo557:CA265_RS24850 Length = 454 Score = 244 bits (624), Expect = 4e-69 Identities = 151/456 (33%), Positives = 238/456 (52%), Gaps = 6/456 (1%) Query: 37 QVINPSNEKVITSVHEATEKDVDVAVAAARAAFEGPWRQVTPSERGILINKLADLMERDI 96 Q+INP+ ++ITS+ E + + A + A + W T ER +I +DL+E +I Sbjct: 2 QIINPATAEIITSLEEDNLSTLQLKFDALQKA-QPQWAGKTLQERIAVITHFSDLLEVEI 60 Query: 97 DTLAAIESLDNGKAFTMAKVDLANSIGCLRYYAGWADKIHGQTIDTN-PETLTYTRHEPV 155 + LA++ + + GK ++ ++ + +++ A+K + T+ P ++EP+ Sbjct: 61 EKLASVLTSEVGKPLQQSRNEINGARARIKWMLANAEKYLADEVMTDEPGIKEIIKYEPL 120 Query: 156 GVCGQIIPWNFPLLMWSWKIGPAVAAGNTVVLKTAEQTPLSALYAAKLIKEAGFPAGVIN 215 GV I WN+P L+ PA+ +GNTV+ K +E L+ + KL+K+AG P V + Sbjct: 121 GVVCNISAWNYPYLVGVNVFIPALLSGNTVMYKPSEYATLTGIEIEKLLKKAGVPDDVFH 180 Query: 216 VISGFGRTAGAAISSHMDIDKVAFTGSTLVGRTILQAAAKSNLKKVTLELGGKSPNIVFD 275 + G T A ++ MD + FTGS G+ I + A + + LELGGK P + D Sbjct: 181 IAIGAKETGSALLN--MDFNGYFFTGSYKTGKLIYEKVA-AKMVPCQLELGGKDPLYITD 237 Query: 276 DA-DIDNAISWANFGIFFNHGQCCCAGSRILVQEGIYDKFVARFKERAQKNKVGNPFEQD 334 D D+ A G F+N+GQ CCA RI VQE YD + F + K G P + Sbjct: 238 DVTDVAAAAIGTADGAFYNNGQSCCAVERIYVQEKNYDDYCNAFVTEVKSWKTGIPTAEG 297 Query: 335 TFQGPQVSQLQFDRIMEYINHGKKAGATVATGGDRHGNEGYFIQPTVFTDVTSDMKIAQE 394 + G + Q + + GA + TGG +GY+ +PTV TDVT+DM + QE Sbjct: 298 VYIGALTRKEQISVLENQVKDALNKGAKLLTGGKAVEGKGYYFEPTVLTDVTNDMLVMQE 357 Query: 395 EIFGPVVTIQKFKDEAEAIKIGNSTDYGLAAAVHTKNVNTAIRVSNALKAGTVWINNYNM 454 E FGP++ I K KD+AEA+K+ TDYGL A+V+T + A ++ L AG+ + N + Sbjct: 358 ESFGPIIGIMKVKDDAEALKMMKDTDYGLTASVYTASQERAEKILAQLDAGSGYWNCCDR 417 Query: 455 ISYQAPFGGFKQSGLGRELGSYALENYTQIKTVHYR 490 +S P+ G K SG+G L + +T+ K H R Sbjct: 418 VSAALPWSGRKYSGIGATLSHQGIRAFTKPKGYHLR 453 Lambda K H 0.318 0.134 0.397 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: 496 Number of extensions: 27 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: 497 Length of database: 454 Length adjustment: 33 Effective length of query: 464 Effective length of database: 421 Effective search space: 195344 Effective search space used: 195344 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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