Align 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized)
to candidate WP_013459096.1 SULKU_RS01190 aldehyde dehydrogenase
Query= BRENDA::P49189 (494 letters) >NCBI__GCF_000183725.1:WP_013459096.1 Length = 471 Score = 242 bits (618), Expect = 2e-68 Identities = 152/459 (33%), Positives = 242/459 (52%), Gaps = 18/459 (3%) Query: 34 PATGRVIATFTCSGEKEVNLAVQNAKAAFKIWSQKSGMERCRILLEAARIIREREDEIAT 93 P GRV++ + A+ A+ A KI + + +RC LL+ A ++E+ +E A Sbjct: 23 PYDGRVVSRAAECSADDARQALIIAQNASKIAKKVALHQRCAWLLDVASKLKEQREEFAR 82 Query: 94 MECINNGKSIFEARLDIDISWQCLEYYAGLAASMAGEHIQ---LPGG--SFGYTRREPLG 148 + C GK I AR+++D + + A +M GE I +P G + Y RRE G Sbjct: 83 VLCDEVGKPITYARIEVDRCIETITLSAETMRTMHGESINTDAMPSGRAAHAYWRREAAG 142 Query: 149 VCVGIGAWNYPFQIASWKSAPALACGNAMVFKPSPFTPVSALLLAEIYSEAG-VPPGLFN 207 V V I +N+P + + K APAL GNA+V KP+P P+ A LA+++ E+ P + Sbjct: 143 VVVAITPFNFPLNLVAHKLAPALVAGNAVVLKPTPEAPLCAYKLAQLFIESPYATPDALS 202 Query: 208 VVQGGAATGQFLCQHPDVAKVSFTGSVPTGMKIMEMSAKGIKPVTLELGGKSPLIIFSDC 267 VV G A G L +SFTGSV G I+ SA GIK ++LELGG + I + Sbjct: 203 VVYGDAEVGSALVGSDIPRVISFTGSVGVG-NIITRSA-GIKKISLELGGNAATYIDTSA 260 Query: 268 DMNNAVKGALMANFLTQGQVCCNGTRVFVQKEILDKFTEEVVKQTQRIKIGDPLLEDTRM 327 D+ A + F+ GQVC + R++V + D+F ++ + T ++ +G P +DT + Sbjct: 261 DLEYAAARCAIGAFVNSGQVCISLQRIYVDSSVYDEFALKMAEATSKLVVGSPYNDDTFL 320 Query: 328 GPLINRPHLERVLGFVKVAKEQGAKVLCGGDIYVPEDPKLKDGYYMRPCVLTNCRDDMTC 387 GPLIN R + +V+ A E+GA+ L P +G PCV+ + + M Sbjct: 321 GPLINDEAASRAMSWVESAIEEGARAL---------TPPRCEGRIFYPCVMADVTESMKI 371 Query: 388 VKEEIFGPVMSILSFDTEAEVLERANDTTFGLAAGVFTRDIQRAHRVVAELQAGTCFINN 447 V EE+F P++S++ D + + R N++ +GL VFT ++ A + + EL AG IN+ Sbjct: 372 VCEEVFAPIVSLVRVDGIDDAITRMNNSPYGLQFSVFTNNLSHATKAIDELDAGGVVIND 431 Query: 448 YNVSPVEL-PFGGYKKSGFGRENGRVTIEYYSQLKTVCV 485 ++ P+GG K SG GRE R IE ++++K++ + Sbjct: 432 MPTLRFDIQPYGGVKLSGVGREGPRFAIEEFTEIKSIVI 470 Lambda K H 0.320 0.137 0.411 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: 478 Number of extensions: 19 Number of successful extensions: 6 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: 494 Length of database: 471 Length adjustment: 34 Effective length of query: 460 Effective length of database: 437 Effective search space: 201020 Effective search space used: 201020 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: 52 (24.6 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