Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate GFF1150 PGA1_c11650 putative lysine/ornithine decarboxylase
Query= BRENDA::G4XUJ8 (413 letters) >FitnessBrowser__Phaeo:GFF1150 Length = 383 Score = 158 bits (400), Expect = 2e-43 Identities = 119/347 (34%), Positives = 178/347 (51%), Gaps = 26/347 (7%) Query: 74 YAVKCNPEPALLGSLAAMG-ANFDCASRAEIEAVLSLRVSPDRIV-YANPCKQESHIKYA 131 YAVK NP PA+L +L A G FD AS AE++AV + SPD ++ Y NP + + I Sbjct: 49 YAVKANPHPAVLSNLVAAGITGFDVASPAEMDAVRA--ASPDAVMHYNNPVRSDVEIAAG 106 Query: 132 ASVGVNLTTFDSKDELEKMRKWHPKCALLLRVKAPEDGGARCPLGPKYGALPEEVIPLLQ 191 + GV + D EL+K+ C + +R P GA G K+GA P+ I LL+ Sbjct: 107 IAHGVASWSVDEPSELDKLADVPKSCEIAVRFALPV-AGAAYDFGSKFGAEPDMAIELLK 165 Query: 192 AAQAARLSVVGASFHIGSGATHFSSYRGAIAEAKKVFETAVKMGMPRMTMLNIGGGFTAG 251 AA FH G+ S++ + AK++ + A G+ ++ LN+GGGF A Sbjct: 166 RV-AAEGWTPALCFHPGTQCEDESAWVEYVHAAKRIIDAA---GV-KIARLNVGGGFAAN 220 Query: 252 SQ-----FDEAATAIKSALQTYFPNE-PGLTIISEPGRFFAESAFTLATNVIGRRVRGEL 305 ++ AI A+ F ++ PGL I EPGR +FTLA + G R GE+ Sbjct: 221 RDGVAPDLEKVFAAIWVAVDAAFGDDKPGL--ICEPGRAMVSESFTLAARIKGIRKAGEV 278 Query: 306 REYWINDGIYGSMNCILYDHATVTCKPLACTSSRANPMCKGARVYNSTVFGPTCDALDTV 365 ++NDG+YG + I + +A +R +GA VFGPTCD+LD + Sbjct: 279 --VFLNDGVYGGLVDIRDMGLPGRVEVVAADGTR-----RGADAQPRVVFGPTCDSLDRL 331 Query: 366 MTGHLLP-DLQVSDWLVFPNMGAYTAAAGSSFNGFKTAAILTYLAYS 411 G LP D Q+ D+++FP +GAY++A + FNG+ + + T + S Sbjct: 332 PDGLPLPRDTQIGDYVLFPGLGAYSSAMSTQFNGYGLSDVATVIELS 378 Lambda K H 0.320 0.134 0.406 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: 427 Number of extensions: 25 Number of successful extensions: 6 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: 413 Length of database: 383 Length adjustment: 31 Effective length of query: 382 Effective length of database: 352 Effective search space: 134464 Effective search space used: 134464 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 (21.8 bits) S2: 50 (23.9 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