Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate PP_0545 PP_0545 aldehyde dehydrogenase
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__Putida:PP_0545 Length = 506 Score = 323 bits (828), Expect = 8e-93 Identities = 185/480 (38%), Positives = 280/480 (58%), Gaps = 16/480 (3%) Query: 7 INGELVSG-EGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAE 65 I GE V+ +G+ +P G ++ E ++AE +D A+ AA AA WG+T+ + R+ Sbjct: 23 IGGEFVTPVKGQYFENTSPVNGKLIAEFPRSTAEDIDKALDAAHAAADAWGRTSVQDRSN 82 Query: 66 CLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGE 125 LLK+AD IE+N ++ A E+ + GKP+ N +IP VD FR+FAG R G AA E Sbjct: 83 VLLKIADRIEQNLELLAITETWDNGKPIRETLNADIPLAVDHFRYFAGCIRAQEGGAA-E 141 Query: 126 YLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLA 185 EG + +PLGVV I PWN+P++MAAWKLAPALAAGNCVVLKP+E TPL L Sbjct: 142 INEGTVAYHIHEPLGVVGQIIPWNFPILMAAWKLAPALAAGNCVVLKPAEQTPLGITVLL 201 Query: 186 ELAKDIFPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHM 245 E+ D+ P GV+N++ G G+ G+ L ++ ++ TGS G HI+ A +I + + Sbjct: 202 EVIGDLLPPGVLNVVQGYGREAGEALATSKRIAKIAFTGSTPVGSHIMKCAAENIIPSTV 261 Query: 246 ELGGKAPVIVFDD------ADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEK 299 ELGGK+P + F+D + IE EG+ ++N G+ CT R Q+ IY +E Sbjct: 262 ELGGKSPNVYFEDIMQAEPSFIEKAAEGM-VLAFFNQGEVCTCPSRALVQESIYPQFMEV 320 Query: 300 LGAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGG--EKRKGN- 356 + V +K G P D T +G +S E++ ++ A+ G +++TGG EK +G+ Sbjct: 321 VMKKVLQIKRGDPLDTDTMVGAQASQQQFEKILSYLQIAQEEG-AELLTGGKVEKLEGSL 379 Query: 357 --GYYYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKD 414 GYY PTLL G + Q+E+FGPVVSVT F +E + + AND+++GL + VWT+D Sbjct: 380 ATGYYIQPTLLKGN-NKMRVFQEEIFGPVVSVTTFKDEAEALAIANDTEFGLGAGVWTRD 438 Query: 415 VGRAHRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVKH 474 + RA+R+ ++ G W N + + + GG K SG G++ L+ Y ++++V + Sbjct: 439 INRAYRMGRGIKAGRVWTNCYHLYPAHAAFGGYKKSGVGRETHKMMLDHYQQTKNLLVSY 498 Lambda K H 0.317 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: 561 Number of extensions: 25 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: 474 Length of database: 506 Length adjustment: 34 Effective length of query: 440 Effective length of database: 472 Effective search space: 207680 Effective search space used: 207680 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