Align 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized)
to candidate SM_b21301 SM_b21301 ly membrane-anchored aldehyde dehydrogenase
Query= SwissProt::Q9H2A2 (487 letters) >FitnessBrowser__Smeli:SM_b21301 Length = 794 Score = 315 bits (808), Expect = 3e-90 Identities = 170/465 (36%), Positives = 269/465 (57%), Gaps = 21/465 (4%) Query: 10 LENFIDGKFLPCSS--YIDSYDPSTGEVYCRVPNSGKDEIEAAVKAAREAFPSWSSRSPQ 67 L +FI+G F+ +S D+++P+TG++ ++ + G+D++ AAV AAR+A W+ S Sbjct: 33 LGHFINGAFVGSASGKSFDTFEPATGKLLAKIAHGGRDDVNAAVAAARKAQGPWAKLSGH 92 Query: 68 ERSRVLNQVADLLEQSLEEFAQAESKDQGKTLALARTMDIPRSVQNFRFFASSSLHHTSE 127 R+R L +A L+++ A E+ D GK + R +DIP + ++F +H + Sbjct: 93 ARARHLYALARLIQRHARLIAVVEALDNGKPIRETRDIDIPLAARHF--------YHHAG 144 Query: 128 CTQMDHLGCMHYTVRAPVGVAGLISPWNLPLYLLTWKIAPAMAAGNTVIAKPSELTSVTA 187 Q+ + + PVGV G + PWN P +L WK+APA+A GN+VI KP+E T +TA Sbjct: 145 WAQLQET---EFADQVPVGVVGQVIPWNFPFLMLAWKVAPALALGNSVILKPAEFTPLTA 201 Query: 188 WMLCKLLDKAGVPPGVVNIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAPHC 247 + +L AG+PPGV+N+V G G G +V H ++ I+FTGS I + +A Sbjct: 202 LLFAELAAAAGLPPGVLNVVTGEG-ETGALIVEHEDIDKIAFTGSTEVGRLIREKTAGSG 260 Query: 248 KKLSLELGGKNPAIIFEDANLDECIPATVRSSFANQGEICLCTSRIFVQKSIYSEFLKRF 307 K L+LELGGK+P I+F+DA++D + V + + NQG++C SR+ VQ+ + F R Sbjct: 261 KSLTLELGGKSPFIVFDDADIDAAVEGVVDAIWFNQGQVCCAGSRLLVQEGVAPVFHDRL 320 Query: 308 VEATRKWKVGIPSDPLVSIGALISKAHLEKVRSYVKRALAEGAQIWCGEGVDKLSLPARN 367 +VG P D + + A+++ L+++ V + +AEGA + K+ LP Sbjct: 321 KRRMETLRVGHPLDKAIDMAAIVAPVQLQRIEELVAKGVAEGASMH----QPKIELP--- 373 Query: 368 QAGYFMLPTVITDIKDESCCMTEEIFGPVTCVVPFDSEEEVIERANNVKYGLAATVWSSN 427 + G F PT++T ++ S TEEIFGPV + F + EE I+ AN+ +YGLAA+VWS Sbjct: 374 KGGSFFRPTLLTGVQPTSVVATEEIFGPVAVSMTFRTPEEAIQLANHSRYGLAASVWSET 433 Query: 428 VGRVHRVAKKLQSGLVWTNCWLIRELNLPFGGMKSSGIGREGAKD 472 +G VA KL +G+VW N + + + FGG + SG GREG ++ Sbjct: 434 IGLALHVAAKLAAGVVWVNATNLFDASSGFGGKRESGFGREGGRE 478 Score = 91.7 bits (226), Expect = 9e-23 Identities = 75/245 (30%), Positives = 117/245 (47%), Gaps = 6/245 (2%) Query: 13 FIDGKFL-PCSSYIDSYDPSTGEVYCRVPNSGKDEIEAAVKAAREAFPSWSSRSPQERSR 71 F+ GK P +Y G+V V + +I AV AAR A WSS + R++ Sbjct: 522 FVGGKQARPDGNYSRPVLSPKGKVIGEVGEGNRKDIRNAVVAARGA-SGWSSATAHNRAQ 580 Query: 72 VLNQVADLLEQSLEEFAQAESKDQGKTLALARTMDIPRSVQNFRFFASSSLHHTSECT-Q 130 +L +A+ L EFA + G + A AR ++ S+ R F+ + E T Sbjct: 581 ILYYIAENLSSRGAEFAGRIAAMTGASAANARA-EVEASIA--RLFSYGAWADKYEGTVH 637 Query: 131 MDHLGCMHYTVRAPVGVAGLISPWNLPLYLLTWKIAPAMAAGNTVIAKPSELTSVTAWML 190 L + + P GV G+I P PL L +AP +A GN V+A PSE + A Sbjct: 638 QPPLRGVALAMPEPQGVVGVICPPEAPLLGLVSLVAPLIAVGNRVVAVPSEAHPLAATDF 697 Query: 191 CKLLDKAGVPPGVVNIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAPHCKKL 250 +L+ + VPPGV+NIV G+ + +AL +H +V + GS + + +LS + K+ Sbjct: 698 YSVLETSDVPPGVINIVTGSAIELAKALAAHNDVDALWAFGSPELSTLVEKLSVGNLKRT 757 Query: 251 SLELG 255 ++ G Sbjct: 758 FVDYG 762 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: 869 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: 794 Length adjustment: 37 Effective length of query: 450 Effective length of database: 757 Effective search space: 340650 Effective search space used: 340650 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: 53 (25.0 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