Align arginine deiminase (EC 3.5.3.6) (characterized)
to candidate GFF4046 HP15_3986 arginine deiminase
Query= BRENDA::P13981 (418 letters) >FitnessBrowser__Marino:GFF4046 Length = 409 Score = 464 bits (1194), Expect = e-135 Identities = 226/410 (55%), Positives = 296/410 (72%), Gaps = 7/410 (1%) Query: 8 LGVHSEAGKLRKVMVCSPGLAHQRLTPSNCDELLFDDVIWVNQAKRDHFDFVTKMRERGI 67 LGVHSE G LR+V++C PGLAH+RLTPSNCD LLFDDV WV QA++DH F + MR RG+ Sbjct: 6 LGVHSETGTLRQVIICRPGLAHRRLTPSNCDALLFDDVFWVKQAQKDHDVFASVMRGRGV 65 Query: 68 DVLEMHNLLTETIQNPEALKWILDRKITADSVGLGLTSELRSWLESLEPRKLAEYLIGGV 127 +VL+++ LL ET+ PE WILD +I + +G+G+ S+LR+W++ L + LAE+LIGG+ Sbjct: 66 EVLDVNELLAETLAIPEGRAWILDHRINWNHIGVGMVSDLRAWMDELPEKALAEFLIGGL 125 Query: 128 AADDLPASEGANILKMYREYLGHSSFLLPPLPNTQFTRDTTCWIYGGVTLNPMYWPARRQ 187 DLP + ++ +LG F+LPPLPN FTRD + W+YGGVTLNPMYW AR+ Sbjct: 126 EVGDLPFDP----VGLFGNHLGRFGFVLPPLPNFLFTRDNSAWVYGGVTLNPMYWVARKP 181 Query: 188 ETLLTTAIYKFHPEFANAEFEIWYGDPDKDHGSSTLEGGDVMPIGNGVVLIGMGERSSRQ 247 ETLL AIY+FHP+FA + + +GDP +DHG +TLEGGD+MP+GN VL+GMGERSS Q Sbjct: 182 ETLLMAAIYRFHPKFA-GKVNVHWGDPLEDHGLATLEGGDIMPLGNRTVLVGMGERSSPQ 240 Query: 248 AIGQVAQSLFAKGAAERVIVAGLPKSRAAMHLDTVFSFCDRDLVTVFPEVVKEIVPFSLR 307 AIGQ++++LF G +RVI LPK+R+AMHLDTVF+FC ++VT F EV ++ + LR Sbjct: 241 AIGQLSKALFDGGMVDRVIACQLPKTRSAMHLDTVFTFCGGNVVTAFKEVADAVICYDLR 300 Query: 308 PDPSSPYGMNIRREEKTFLEVVAESLGLKKLRVVETGGNS-FAAEREQWDDGNNVVCLEP 366 P + + ++ + EVVAE LG L VV TGG++ EREQW+DGNNV+ L P Sbjct: 301 PGEGAK-TLAFNQDSRHLFEVVAEILGYPALEVVPTGGDTPEEREREQWNDGNNVLALSP 359 Query: 367 GVVVGYDRNTYTNTLLRKAGVEVITISASELGRGRGGGHCMTCPIVRDPI 416 GVVVGYDRN TN L AG+EV+ I +ELGRGRGGG CM+CP +RD I Sbjct: 360 GVVVGYDRNDDTNAALSAAGIEVLAIPGAELGRGRGGGRCMSCPTIRDAI 409 Lambda K H 0.319 0.137 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: 554 Number of extensions: 13 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: 418 Length of database: 409 Length adjustment: 31 Effective length of query: 387 Effective length of database: 378 Effective search space: 146286 Effective search space used: 146286 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: 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