Align Phenylacetaldehyde dehydrogenase; PAD; EC 1.2.1.39 (characterized)
to candidate WP_011385953.1 AMB_RS18195 DUF1487 domain-containing protein
Query= SwissProt::O06837 (502 letters) >NCBI__GCF_000009985.1:WP_011385953.1 Length = 496 Score = 333 bits (853), Expect = 1e-95 Identities = 205/498 (41%), Positives = 280/498 (56%), Gaps = 20/498 (4%) Query: 12 PAIDGLRLPHQM----LIGGQWVNAQSDKTLNVYNPATGDTLTDVPDGDVEDVNAAVESA 67 P +D +L + LIGG+ V A + V NPATG+ + G EDV+ AV SA Sbjct: 5 PELDPFKLAKALSGKHLIGGKLVPAGCGEVFEVDNPATGEIIGTAAFGTKEDVDIAVISA 64 Query: 68 AATLQSDAWRRMPPSARERILLRLADLLEAHGDELARLETLNNGKLLIYSKMMEVGASAQ 127 A Q D W + AR +++ +L AH +EL RL L GK L +E G A Sbjct: 65 KAA-QKD-WAKQSARARGKLVAECGRVLSAHVEELGRLVALETGKALRTESRVEAGVLAD 122 Query: 128 WLRYMAGWATKLTGSTLDLSLPLPPDVRSRASTQRVPVGVVAAIIPWNFPLLMAVWKIAP 187 + G ++L G T+ P PD+ + T R PVGVV IIPWN PLL+ K A Sbjct: 123 MFTFFGGLGSELKGETI----PFNPDMLT--VTVREPVGVVGCIIPWNVPLLLMAMKAAA 176 Query: 188 ALACGNTVVLKPAEETPLTALRLAELAMEAGLPAGALNVVTGRGETAGDALVRHPKVAKV 247 AL GN+VV+K AEE PLT LR+AE+ M LP G N+++G G G LV HP V KV Sbjct: 177 ALVAGNSVVVKSAEEAPLTVLRVAEI-MNTVLPPGLFNMLSGFGPECGAPLVEHPDVKKV 235 Query: 248 AFTGSTEVGRIIGSACGRSLKAVSLELGGKSPVIVLADCDPQEAAEGAAAAI-FFNHGQV 306 FTGS E GRI+ A L V+LELGGKSP+IV AD D +A GA A + F GQ Sbjct: 236 TFTGSVETGRIVYKAAAEKLIPVTLELGGKSPMIVCADADMDQAVAGALAGMRFTRQGQS 295 Query: 307 CTAGSRLYVHESIYEDVIQRLAVIGESIVVGSGLEQGVHMGPMVSKKHHENVLRHIRNGI 366 CTA SRL+VHESI+++ + ++ +++V+G L++ +G +VS E V +I+ G Sbjct: 296 CTASSRLFVHESIHDEFVAKVKAKVDAMVMGDPLDEKTDIGTIVSDGQLERVRSYIKIGE 355 Query: 367 ED--GADLICGG--TEAPCAQGFFVKPTIFANREKKDIRLLSQEVFGPVLVATPFSDIAE 422 E +C T+ A+G FV+P IF + D RL +E+FGPV +SD + Sbjct: 356 ETKGATKHVCSALPTDPKLAKGRFVQPVIFTGMKNSD-RLCQEEIFGPVCAVIKWSDYED 414 Query: 423 VVNEANRSVYGLGASIWTNDLSAALRINDELEAGTVWVNTHNMVDPNLPFGGFKDSGVGR 482 V+ +AN S YGL ASIWT D A+ LEAG V VN + +V P L +GG K SG+G+ Sbjct: 415 VLAQANDSEYGLAASIWTRDFKLAMDATKRLEAGFVQVNQNLVVQPGLSYGGVKTSGIGK 474 Query: 483 EHG-AAAIEHYTTTRSLV 499 E + +EH+T ++++ Sbjct: 475 EASLESMLEHFTHKKTII 492 Lambda K H 0.317 0.134 0.395 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: 575 Number of extensions: 23 Number of successful extensions: 7 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: 502 Length of database: 496 Length adjustment: 34 Effective length of query: 468 Effective length of database: 462 Effective search space: 216216 Effective search space used: 216216 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 (21.7 bits) S2: 52 (24.6 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