Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate 3608018 Dshi_1425 aldehyde dehydrogenase (RefSeq)
Query= BRENDA::Q5P171 (474 letters) >FitnessBrowser__Dino:3608018 Length = 484 Score = 405 bits (1041), Expect = e-117 Identities = 210/466 (45%), Positives = 288/466 (61%), Gaps = 4/466 (0%) Query: 8 INGKPVRAGSTFDVVNPATGEVFARVQAGDASHVDQAVAAARAAFPGWSRTPDAERKRLM 67 ING V + +F+V NPAT EV A V+QA+AAA+AA PGW+ ER + Sbjct: 23 INGALVDSAGSFEVFNPATDEVVAHAPNASRDQVEQAIAAAKAAQPGWAALSQDERGAYI 82 Query: 68 HALGAALEAHMPELMELVTKEAGKPLGGLNGVGSGMEVGGAIAWTHVTADLELPVEVIQD 127 A AL+AH EL+ L+T E GKP + + EV AI W A L EVI+D Sbjct: 83 AAYADALDAHKQELITLLTTEQGKPRHSM----ATTEVEYAIFWVREVAKRRLEDEVIED 138 Query: 128 NDDARIEVHRKPLGVVGSITPWNWPLMIAIWHVIPALRAGNTVVIKPSGMTPTATIRFVE 187 + ++V PLGVVG+ITPWN+P+++ +W + P L GNT+V+KPS TP T+RF E Sbjct: 139 TPEHTVKVAHTPLGVVGAITPWNFPVLLGLWKIAPCLVTGNTMVMKPSPYTPLCTLRFGE 198 Query: 188 LANAILPPGVLNIVTGESGVGSAIAKHPDINKIVFTGSTPTGKNIMQNAAGNLKRLTLEL 247 +A + P GVLN+V G + G+ + +HPDI KI FTGST TG+ +M +++ NLKR+TLEL Sbjct: 199 IAQQVFPAGVLNVVAGGNEQGAWLTEHPDIAKISFTGSTATGRKVMASSSCNLKRITLEL 258 Query: 248 GGNDAGIVLPDVDPKAIAPKLFGVGFHNNGQTCACLKRLYVHDSIYEKVCAELARIAKET 307 GGND I+LP D K + P LF + N+GQ C +KRLYVH+S+Y+ + A E Sbjct: 259 GGNDPAILLPGTDYKPLIPTLFDAAYGNSGQWCIAVKRLYVHESLYDDFLRDFVAHAAEK 318 Query: 308 VVGDGLVEGTELGPVQNKAQLDFVQELVEDARAHGARILSGGKARSGGGFFFEPTVIADA 367 VG+G+ T+LGP+QNK Q +++L D +A G + GG+ G G F T++ + Sbjct: 319 TVGNGMDPNTDLGPIQNKMQYGKLKDLFADVKAQGLSVPLGGEIPDGPGNFVPITIVDNP 378 Query: 368 KDGMRVVDEEQFGPVLPVIRYSDIEEVIARANNNENGLGGSIWSKDHAKAAELALRLECG 427 RVV EE FGP+LP+I++SD++EV+ AN+ E GL S+W D A +A RLE G Sbjct: 379 PKDSRVVREEPFGPILPIIKWSDLDEVVRDANDTEFGLAASVWGPDRDTAIGVANRLEAG 438 Query: 428 TAWVNEHGAVQPDAPFGGVKQSGLGVEFGRYGLEEYTSIQTLKIMK 473 T WVNE D PFGG KQSG+GVE G+ GL+E+T+ +T K Sbjct: 439 TVWVNEIHIHGIDIPFGGHKQSGMGVENGQEGLKEFTNTKTYMFRK 484 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: 694 Number of extensions: 31 Number of successful extensions: 2 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: 484 Length adjustment: 34 Effective length of query: 440 Effective length of database: 450 Effective search space: 198000 Effective search space used: 198000 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