Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate Ga0059261_1680 Ga0059261_1680 NAD-dependent aldehyde dehydrogenases
Query= BRENDA::Q5P171 (474 letters) >FitnessBrowser__Korea:Ga0059261_1680 Length = 469 Score = 554 bits (1428), Expect = e-162 Identities = 270/468 (57%), Positives = 341/468 (72%), Gaps = 5/468 (1%) Query: 6 MIINGKPVRAGSTFDVVNPATGEVFARVQAGDASHVDQAVAAARAAFPGWSRTPDAERKR 65 +I++GKP+ TF V++PATG FA + +D AVAAAR AFPGW+ TP +R Sbjct: 6 LIVDGKPLAMAETFPVIDPATGRPFADAPLASTADLDAAVAAARRAFPGWAATPIEDRAA 65 Query: 66 LMHALGAALEAHMPELMELVTKEAGKPLGGLNGVGSGMEVGGAIAWTHVTADLELPVEVI 125 + A+ ++EA EL L++ E GKP+ N VG E+ GA+AW TA L V+V+ Sbjct: 66 AILAIADSIEAAKDELARLLSAEQGKPVP--NAVG---EIMGALAWARATAGLRPAVDVL 120 Query: 126 QDNDDARIEVHRKPLGVVGSITPWNWPLMIAIWHVIPALRAGNTVVIKPSGMTPTATIRF 185 +D+D R+EVHRKPLGVV SI+PWN+P+MIAIWH+IP L AGNTVV+KPS TP A +R Sbjct: 121 KDDDSVRVEVHRKPLGVVASISPWNFPVMIAIWHIIPGLVAGNTVVMKPSSFTPLAALRM 180 Query: 186 VELANAILPPGVLNIVTGESGVGSAIAKHPDINKIVFTGSTPTGKNIMQNAAGNLKRLTL 245 VE+ANA LPPGVLN VTGE +G AIA HP I+KIVFTGSTPTG++IM + A NLKRLTL Sbjct: 181 VEIANAHLPPGVLNSVTGEVEIGRAIASHPGIDKIVFTGSTPTGRSIMADGAANLKRLTL 240 Query: 246 ELGGNDAGIVLPDVDPKAIAPKLFGVGFHNNGQTCACLKRLYVHDSIYEKVCAELARIAK 305 ELGGNDA IVLPD D +A K+F F N+GQ CA +KR+YVH+SI++ + +LA +A+ Sbjct: 241 ELGGNDAAIVLPDADVDKVAAKIFAKAFGNSGQICAAVKRVYVHESIHDALAEKLAEMAR 300 Query: 306 ETVVGDGLVEGTELGPVQNKAQLDFVQELVEDARAHGARILSGGKARSGGGFFFEPTVIA 365 VVG G ++ GPVQN+ Q D V+ L +DARAHG R L+GG+AR G G+FF +V+ Sbjct: 301 TAVVGPGSDAASQFGPVQNRKQFDLVRALADDARAHGGRFLAGGEAREGDGYFFPLSVVV 360 Query: 366 DAKDGMRVVDEEQFGPVLPVIRYSDIEEVIARANNNENGLGGSIWSKDHAKAAELALRLE 425 D DGMR+VDEEQFGP+LPVIRYSD E+ +ARAN NENGLGGS+WS D A A A RLE Sbjct: 361 DVTDGMRIVDEEQFGPILPVIRYSDPEDALARANANENGLGGSVWSADPAAALAFAQRLE 420 Query: 426 CGTAWVNEHGAVQPDAPFGGVKQSGLGVEFGRYGLEEYTSIQTLKIMK 473 GT WVN+H ++ PD PFGG KQSG+G EFG YGLEEY +QT+++ K Sbjct: 421 AGTVWVNDHASISPDVPFGGAKQSGVGTEFGLYGLEEYMQLQTVRVAK 468 Lambda K H 0.317 0.136 0.405 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: 749 Number of extensions: 48 Number of successful extensions: 3 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: 469 Length adjustment: 33 Effective length of query: 441 Effective length of database: 436 Effective search space: 192276 Effective search space used: 192276 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 (21.6 bits) S2: 51 (24.3 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