Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate PP_1481 PP_1481 medium chain aldehyde dehydrogenase
Query= BRENDA::Q5P171 (474 letters) >FitnessBrowser__Putida:PP_1481 Length = 474 Score = 329 bits (844), Expect = 1e-94 Identities = 193/482 (40%), Positives = 263/482 (54%), Gaps = 30/482 (6%) Query: 6 MIINGKPVRA-GSTFDVVNPATGEVFARVQAGDASHVDQAVAAARAAFPGWSRTPDAERK 64 M+ING+ V G + V+NPA G A++ + VD AV AA AF WS+T ER Sbjct: 5 MLINGQLVAGQGPAWTVLNPALGTALAQINEATEAQVDSAVRAADQAFDSWSQTSPKERS 64 Query: 65 RLMHALGAALEAHMPELMELVTKEAGKPLGG-LNG------------VGSGMEVGGAIAW 111 + + AL A+EAH EL L ++ GKPL LN G+ +GG+ A Sbjct: 65 QALLALADAIEAHGDELARLESQNCGKPLSAALNDEIPAIADVFRFFAGAARCLGGSAAG 124 Query: 112 THVTADLELPVEVIQDNDDARIEVHRKPLGVVGSITPWNWPLMIAIWHVIPALRAGNTVV 171 ++ + + R PLGVV SI PWN+PLM+ W + PAL AGNTVV Sbjct: 125 EYLPGHTSM--------------IRRDPLGVVASIAPWNYPLMMLAWKIAPALAAGNTVV 170 Query: 172 IKPSGMTPTATIRFVELANAILPPGVLNIVTGESG-VGSAIAKHPDINKIVFTGSTPTGK 230 IKPS +TP +R ELA +LPPGVLNI+ G VG+ + HP + + TGS PTG Sbjct: 171 IKPSELTPLTALRLGELAQDLLPPGVLNILFGRGQTVGNPLITHPKVRMVSLTGSIPTGA 230 Query: 231 NIMQNAAGNLKRLTLELGGNDAGIVLPDVDPKAIAPKLFGVGFHNNGQTCACLKRLYVHD 290 +I+ A ++KR+ +ELGG +V D D A + GF+N GQ C RLYV D Sbjct: 231 HIISATADSVKRMHMELGGKAPVLVFDDADIDAAIDGIRTFGFYNAGQDCTAACRLYVQD 290 Query: 291 SIYEKVCAELARIAKETVVGDGLVEGTELGPVQNKAQLDFVQELVEDARAHG-ARILSGG 349 IYE+ L + G E TELGP+ + D V LV+ A A R+++GG Sbjct: 291 GIYERFVERLGKAVASLKPGLQESEETELGPLISAQHRDKVAGLVQRAIAQPHIRLVTGG 350 Query: 350 KARSGGGFFFEPTVIADAKDGMRVVDEEQFGPVLPVIRYSDIEEVIARANNNENGLGGSI 409 K +G GFFFEPTV+ADA +V E FGPV+ V R++D + + AN++ GL S+ Sbjct: 351 KPIAGDGFFFEPTVLADALQDDEIVRNEVFGPVVSVTRFTDEAQALEWANDSNYGLASSV 410 Query: 410 WSKDHAKAAELALRLECGTAWVNEHGAVQPDAPFGGVKQSGLGVEFGRYGLEEYTSIQTL 469 W++D +A LA RL+ G WVN H + + P GG K SG G + YGLE+YT ++ + Sbjct: 411 WTRDTGRAHRLAARLQYGCTWVNTHFMLVSEMPHGGQKHSGYGKDMSMYGLEDYTCVRHV 470 Query: 470 KI 471 I Sbjct: 471 MI 472 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: 621 Number of extensions: 23 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: 474 Length of database: 474 Length adjustment: 33 Effective length of query: 441 Effective length of database: 441 Effective search space: 194481 Effective search space used: 194481 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