Align 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized)
to candidate N515DRAFT_3729 N515DRAFT_3729 aminomuconate-semialdehyde/2-hydroxymuconate-6-semialdehyde dehydrogenase
Query= SwissProt::Q9H2A2 (487 letters) >FitnessBrowser__Dyella79:N515DRAFT_3729 Length = 483 Score = 473 bits (1217), Expect = e-138 Identities = 237/483 (49%), Positives = 330/483 (68%), Gaps = 6/483 (1%) Query: 8 LMLENFIDGKFLPCSS--YIDSYDPSTGEVYCRVPNSGKDEIEAAVKAAREAFPSWSSRS 65 L L N IDG+ +++ ++P+TGEV+ P S +++AAV AA A P W++ Sbjct: 4 LRLANLIDGRLQAPRQERWLEVFEPATGEVFAHCPESSFADVDAAVAAAVAAAPGWAATP 63 Query: 66 PQERSRVLNQVADLLEQSLEEFAQAESKDQGKTLALARTMDIPRSVQNFRFFASSSLHHT 125 ++R+R+L ++ADL+E L+EFA ES+D GK L+LAR++DIPR+V N R+FA++ + + Sbjct: 64 SEQRARLLQRLADLIEARLDEFAALESRDSGKPLSLARSLDIPRAVSNLRYFAAAIVPWS 123 Query: 126 SECTQMDHLGCMHYTVRAPVGVAGLISPWNLPLYLLTWKIAPAMAAGNTVIAKPSELTSV 185 SE M+ LG ++YT+R P+GV ISPWNLPLYL TWKIAPA+AAGN V+AKPSE+T Sbjct: 124 SESHAME-LGAINYTLRQPLGVVACISPWNLPLYLFTWKIAPALAAGNAVVAKPSEITPC 182 Query: 186 TAWMLCKLLDKAGVPPGVVNIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAP 245 TA +L +L +AG PPGV+NIV G GP VG+ALV H +V +SFTGS T +I +AP Sbjct: 183 TAALLGELSIEAGFPPGVLNIVQGRGPEVGQALVEHRDVKAVSFTGSTRTGAQIAAAAAP 242 Query: 246 HCKKLSLELGGKNPAIIFEDANL-DECIPATVRSSFANQGEICLCTSRIFVQKSIYSEFL 304 KKLSLELGGKNPAI+F DA+L D + VRS FANQGEICLC SR+ VQ+SIY F Sbjct: 243 RFKKLSLELGGKNPAIVFADADLSDANLDTIVRSGFANQGEICLCGSRLLVQRSIYDAFR 302 Query: 305 KRFVEATRKWKVGIPSDPLVSIGALISKAHLEKVRSYVKRALAEGAQIWCGEGVDKLSLP 364 +R++ R +VG P + +GAL+S+ H +KV + +A AEG ++ CG D L+LP Sbjct: 303 ERYLAKVRALRVGDPREAATDLGALVSREHFDKVTGCIAQARAEGGRVLCGG--DALALP 360 Query: 365 ARNQAGYFMLPTVITDIKDESCCMTEEIFGPVTCVVPFDSEEEVIERANNVKYGLAATVW 424 G+++ PTVI + E+ +EIFGPV ++PFD E + + AN YGLAA++W Sbjct: 361 GPLAGGWYVAPTVIEGLGPETATNQQEIFGPVVTLIPFDDEAQALAIANGTGYGLAASLW 420 Query: 425 SSNVGRVHRVAKKLQSGLVWTNCWLIRELNLPFGGMKSSGIGREGAKDSYDFFTEIKTIT 484 ++++ R HR +L G+VW NCWL+R+L PFGG K SG+GREG ++ FFTE K I Sbjct: 421 TTDLSRAHRFGAQLDFGIVWINCWLLRDLRTPFGGAKQSGVGREGGVEALRFFTEPKNIC 480 Query: 485 VKH 487 +++ Sbjct: 481 IRY 483 Lambda K H 0.319 0.133 0.404 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: 625 Number of extensions: 25 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: 487 Length of database: 483 Length adjustment: 34 Effective length of query: 453 Effective length of database: 449 Effective search space: 203397 Effective search space used: 203397 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 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