Align 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized)
to candidate GFF3227 PGA1_c32800 aldehyde dehydrogenase
Query= SwissProt::Q9H2A2 (487 letters) >FitnessBrowser__Phaeo:GFF3227 Length = 802 Score = 295 bits (756), Expect = 3e-84 Identities = 172/470 (36%), Positives = 257/470 (54%), Gaps = 22/470 (4%) Query: 12 NFIDGKFLPCSSYIDSYDPSTGEVYCRVPNSGKDEIEAAVKAAREAFPSWSSRSPQERSR 71 +FI+G+F DS +P+TGEV + + + ++++AV AAR+A WS+ R+R Sbjct: 59 HFINGEFTAPGDGFDSKNPATGEVLATLSQATQSDVDSAVDAARKAQTKWSAAGGAARAR 118 Query: 72 VLNQVADLLEQSLEEFAQAESKDQGKTLALARTMDIPRSVQNFRFFASSSLHHTSECTQM 131 L +A L+++ FA E+ D GK + +R +D+P + ++F + A + SE Sbjct: 119 YLYAIARLMQKHARLFAVLETLDNGKPIRESRDIDVPLAQRHFYYHAGMAQLMESELPD- 177 Query: 132 DHLGCMHYTVRAPVGVAGLISPWNLPLYLLTWKIAPAMAAGNTVIAKPSELTSVTAWMLC 191 R +GV G I PWN PL +L WK+APA+A GNTV+ KP+E TS+TA + Sbjct: 178 ----------REALGVCGQIIPWNFPLLMLAWKVAPAIAMGNTVVLKPAEYTSLTALLFA 227 Query: 192 KLLDKAGVPPGVVNIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAPHCKKLS 251 + +AG+P GVVNIV G G VGE +V +V I+FTGS RI + +A K L+ Sbjct: 228 DICRQAGLPKGVVNIVTGDGA-VGEMIVG-ADVDKIAFTGSTAVGRRIREATAGSGKALT 285 Query: 252 LELGGKNPAIIFEDANLDECIPATVRSSFANQGEICLCTSRIFVQKSIYSEFLKRFVEAT 311 LELGGK+P I+F+DA++D I V + + NQG++C SR+ VQ+ I F + Sbjct: 286 LELGGKSPYIVFDDADIDSAIEGLVDAIWFNQGQVCCAGSRLLVQEGIAERFHTKLRVRM 345 Query: 312 RKWKVGIPSDPLVSIGALISKAHLEKVRSYVKRALAEGAQIWCGEGVDKLSLPARNQAGY 371 K ++G P D + +GA++ L + V A ++++P R G Sbjct: 346 DKLRIGNPLDKSIDVGAIVDPVQLTTISEMVAANTAGRMH------QAQVAVPER---GC 396 Query: 372 FMLPTVITDIKDESCCMTEEIFGPVTCVVPFDSEEEVIERANNVKYGLAATVWSSNVGRV 431 F PT+I + M EEIFGPV F + E +E ANN +YGLAAT+W+ NV Sbjct: 397 FYPPTLIEGLAPSDALMQEEIFGPVLVSTTFRTPSEAVELANNTRYGLAATLWTENVNLA 456 Query: 432 HRVAKKLQSGLVWTNCWLIRELNLPFGGMKSSGIGREGAKDSYDFFTEIK 481 +A KL +G+VW N + + FGG + SG GREG + +T+ K Sbjct: 457 LDIAPKLVAGVVWVNATNLFDAAAGFGGTRESGFGREGGWEGLSAYTKPK 506 Score = 70.1 bits (170), Expect = 3e-16 Identities = 58/230 (25%), Positives = 104/230 (45%), Gaps = 5/230 (2%) Query: 20 PCSSYIDSYDPSTGEVYCRVPNSGKDEIEAAVKAAREAFPSWSSRSPQERSRVLNQVADL 79 P Y + +G + V + ++ AV+AA A +WS + R+++L + + Sbjct: 543 PDGGYSKAIHSKSGGLLGHVGLGNRKDVRNAVEAAAGA-NAWSKTTGHLRAQILYYIGEN 601 Query: 80 LEQSLEEFAQAESKDQGKTLALARTMDIPRSVQNFRFFASSSLHHTSECTQMDHLGCMHY 139 L + EFA + GK+ ++ S+Q A+ + + + + G + Sbjct: 602 LSARVGEFADRIDRMTGKSQG---AQEVEASIQRLFTAAAWADKYDGQAHGVPIRG-VAL 657 Query: 140 TVRAPVGVAGLISPWNLPLYLLTWKIAPAMAAGNTVIAKPSELTSVTAWMLCKLLDKAGV 199 ++ PVGV G + PL L +APA+A GN V+ SE ++A ++L+ + + Sbjct: 658 AMKEPVGVIGALCADEAPLLGLVSVMAPAIAMGNRVVLAASEAYPLSATDFYQVLETSDL 717 Query: 200 PPGVVNIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAPHCKK 249 P GVVNI+ G + L SH V + S + I + SA + K+ Sbjct: 718 PGGVVNILTGRHAEMASPLASHLNVDAVWSFSSSDLSAMIEEASAGNLKR 767 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: 884 Number of extensions: 35 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 487 Length of database: 802 Length adjustment: 37 Effective length of query: 450 Effective length of database: 765 Effective search space: 344250 Effective search space used: 344250 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: 54 (25.4 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