Align phenylpyruvate decarboxylase (EC 4.1.1.43) (characterized)
to candidate N515DRAFT_1617 N515DRAFT_1617 indolepyruvate decarboxylase
Query= BRENDA::Q2UKV4 (570 letters) >FitnessBrowser__Dyella79:N515DRAFT_1617 Length = 590 Score = 200 bits (509), Expect = 1e-55 Identities = 169/581 (29%), Positives = 272/581 (46%), Gaps = 63/581 (10%) Query: 16 VAEYLFRRLREVGVRAVHGVPGDYN---LVALDYLPKCDLHWVGNCNELNAGYAADGYAR 72 VA+YL RL+++ V V +PGDY AL+Y ++ +G NEL+A YAAD YAR Sbjct: 27 VADYLLTRLKQLNVTDVFQIPGDYVKHFTQALEYFD--GVNTIGAINELDAAYAADAYAR 84 Query: 73 INGMSALVTTFGVGELSALNAIAGAYSEFVPIVHIVGQPHTK----SQKDGMLLHHTLGN 128 G++A+ FGV SALNAIAGA+ E PIV I P + +L HH+ Sbjct: 85 TRGLAAVSLQFGVSTYSALNAIAGAWVERSPIVVISATPGADMRDITDMYDVLFHHS--T 142 Query: 129 GDFNVFTRMSADISCTLGCLNSTHEVATLIDNAIRECWIRSRPVYISLPTDMVTKKIEGE 188 GD N + ++ L++ A ID + + RPVYI+ K++ G+ Sbjct: 143 GDLNSDRAIYEYVTVKAITLSTNVGAAEQIDELLVDAITEKRPVYIA-----CYKEVWGQ 197 Query: 189 RLDTPLDLSLPPNDPEKEDY----VVDVVLKYLHAAKKPVILVDACAIRHRVLDEVHEFV 244 + P L P + VD + AK P+I +R + + + + Sbjct: 198 PCERPPATPLKPRVTRSPELALRNAVDQAWAMITQAKSPLIFAGVEVLRFGLSGLLQKII 257 Query: 245 EKSGLPTFVAPMGKGAVDETHKNYGGVYAGTGSNPGVREQVESSDLILSIGAIKSDFNTT 304 + SG +GK +DE + G Y+ S VRE V +SD +L++GAI +D T Sbjct: 258 DASGFLYTTTTLGKSVLDEQGDKFIGTYSDAASIEAVREIVMASDCVLTLGAIITDDYLT 317 Query: 305 GFSYRIGQLNTIDFHSTYVRVRYSEYPDINMKGVLQKIVQRMGNLNVGPV---SPPSNLL 361 + + D + VR Y +Y D+ M+ ++ ++ R P+ +PP Sbjct: 318 FIEAKYADMVLAD--TAGVRAGYFKYGDVTMRDFMEALLARFTASKAYPIKAKAPPQPKY 375 Query: 362 PDNEKASTE-------QAITHAWLWPTVGQWLKEKDVVITETGTANFGIWDTRFPA---- 410 P A+++ Q IT+ + ++L++KD++ + +G+ + + A Sbjct: 376 PQPWAANSDPVYDAQPQIITYNRFFAHTMKFLQDKDLL--KDIVMTYGVSSSMYVATNCY 433 Query: 411 GV---TAISQVLWGSIGYSVGACQGAALAAKEQGRRTVLFVGDGSFQLTLQEVSTMIRNN 467 G+ + +S W IG+ GA GA L + G+R GDG F + Q +ST+ RN Sbjct: 434 GLKQGSFVSSAAWQCIGFETGAACGAQLGS---GKRAWTVAGDGGFMMVCQSLSTLARNQ 490 Query: 468 LNPIIFVICNEGYTIER-YI----------HGWEAVYNDIQPWDFLNIPVAFGAKDKYKG 516 LN +IFV+ N+ Y IE+ Y+ H ++A ++ + WD+L + AFGA +G Sbjct: 491 LNAVIFVMSNQVYAIEQVYVDMSAFKPGPKHKFDA-FDILPKWDYLALAKAFGA----EG 545 Query: 517 YKVTTRDELRELFAN-EEFASAPCLQLVELHMPRDDCPASL 556 +V T DEL + P LVE+ +P+ D P + Sbjct: 546 IRVETVDELNAALPRIAKIKDKPV--LVEVVIPQKDLPGQM 584 Lambda K H 0.319 0.136 0.414 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: 698 Number of extensions: 40 Number of successful extensions: 5 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: 570 Length of database: 590 Length adjustment: 36 Effective length of query: 534 Effective length of database: 554 Effective search space: 295836 Effective search space used: 295836 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 (21.7 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