Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate AO353_15035 AO353_15035 aldehyde dehydrogenase
Query= BRENDA::Q9EQ20 (535 letters) >FitnessBrowser__pseudo3_N2E3:AO353_15035 Length = 496 Score = 178 bits (452), Expect = 4e-49 Identities = 144/486 (29%), Positives = 233/486 (47%), Gaps = 24/486 (4%) Query: 38 PTVKLFIDGKFVESKSDKWIDIHNPATNEVVGRVPQSTKAEMDAAVESCKRAFPA--WAD 95 PT L I+GK ++S + NPAT V+ V A++DAAV S ++AF + W+ Sbjct: 17 PTQAL-IEGKQRPAQSGQTFAAINPATGAVLAEVAACGNADVDAAVISARQAFESGVWSA 75 Query: 96 TSILSRQQVLLRYQQLIKENLKEIARLITLEQGKTLADAEG-DVFRGLQVVEHACSVTSL 154 S R+QVLLR +LI N +E+A L +L GK + DA DV V Sbjct: 76 RSPGERKQVLLRLAELIMANREELALLDSLNMGKPVMDAYTIDVPGAAGVFRWYAESLDK 135 Query: 155 MLGETMPSITKDMDLYSYRLPLGVCAGIAPFNFPAMIPLWMFPMAMVCGNTFLMKPSERV 214 + + PS + + R LGV A + P+NFP + W A+ GN+ ++KP+E+ Sbjct: 136 LYDQIAPSAQNVLATIT-REALGVVAAVVPWNFPLDMAAWKLAPALAAGNSVILKPAEQS 194 Query: 215 PGATMLLAKLLQDSGAPDGTLNIIHG-QHDAVNFICDHPDIKAISFVGSNQAGEYIFERG 273 P + + L +L ++G P G LN++ G A + H DI + F GS + G+Y + Sbjct: 195 PFSALRLGELALEAGVPPGVLNVLPGLGEQAGKALGLHLDIDCLVFTGSTEVGKYFMQYS 254 Query: 274 SR-NGKRVQANMGAKNHGVVMPDANKENTLNQLVGAAFGA---AGQRCMALSTAILVGEA 329 ++ N K+V G K+ +V D + Q AAFG G+ C A S ++ Sbjct: 255 AQSNLKQVWLECGGKSANLVFADCQDLDLAAQ--KAAFGIFFNQGEVCSANSRLLV---E 309 Query: 330 KKWLPELVDR--AKNLRVNAGD--QPGADLGPLITPQAKERVCNLIDSGTKEGASILLDG 385 + E V+R + R GD + G ++ + R+ I ++GA + G Sbjct: 310 RSIHDEFVERLMVQVERWQPGDPLDSSSTAGAIVDSRQTARIMKFIQQAERQGAKRVCGG 369 Query: 386 RRIKVKGYENGNFVGPTIISNVKPSMTCYKEEIFGPVLVVLETETLDEAIKIVNDNPYGN 445 ++ + G + NF+ PTI + V M +++E+FGPVL V + A+++ ND+ YG Sbjct: 370 QQSIING--SDNFIQPTIFTGVTADMPLFRDEVFGPVLAVTAFDDEASALQLANDSVYGL 427 Query: 446 GTAIFTTNGATARKYAHMVDVGQVGVNVPIPVPLPMFSFTGSRSSFRGDTNFYGKQGIQF 505 +++T + A + A + G V VN + + + G +S F D + + Sbjct: 428 AASLWTDDLNRAHRVARQLRAGTVSVNSVDALDVTVPFGGGKQSGFGRDLSLH---SFDK 484 Query: 506 YTQLKT 511 YTQLKT Sbjct: 485 YTQLKT 490 Lambda K H 0.318 0.133 0.391 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: 515 Number of extensions: 22 Number of successful extensions: 5 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: 535 Length of database: 496 Length adjustment: 35 Effective length of query: 500 Effective length of database: 461 Effective search space: 230500 Effective search space used: 230500 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: 52 (24.6 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