Align arginine deiminase (EC 3.5.3.6) (characterized)
to candidate 3607011 Dshi_0432 Arginine deiminase (RefSeq)
Query= BRENDA::P13981 (418 letters) >FitnessBrowser__Dino:3607011 Length = 409 Score = 478 bits (1229), Expect = e-139 Identities = 231/411 (56%), Positives = 296/411 (72%), Gaps = 7/411 (1%) Query: 7 KLGVHSEAGKLRKVMVCSPGLAHQRLTPSNCDELLFDDVIWVNQAKRDHFDFVTKMRERG 66 KLGVHSE G LR+V++C PGLAH+RLTP NC+ELLFDDV WV QAK+DH F M + G Sbjct: 5 KLGVHSETGTLRQVIICRPGLAHRRLTPENCEELLFDDVFWVKQAKQDHEAFGAAMTQEG 64 Query: 67 IDVLEMHNLLTETIQNPEALKWILDRKITADSVGLGLTSELRSWLESLEPRKLAEYLIGG 126 ++VLE LL ET++ PEA KW+LD +I+A+ VG+G+ +LR W++ L +LA +LIGG Sbjct: 65 VEVLETGALLGETLEIPEARKWVLDHRISANDVGVGMRKDLRDWMDELPGTELATWLIGG 124 Query: 127 VAADDLPASEGANILKMYREYLGHSSFLLPPLPNTQFTRDTTCWIYGGVTLNPMYWPARR 186 + D+P M+ YLG F+LPPLPN FTRD + W+YGGVTLNPMYW ARR Sbjct: 125 LTVGDVP----FEATSMFGAYLGRHGFILPPLPNFLFTRDNSSWVYGGVTLNPMYWQARR 180 Query: 187 QETLLTTAIYKFHPEFANAEFEIWYGDPDKDHGSSTLEGGDVMPIGNGVVLIGMGERSSR 246 ETLLT AIY++HP+FA EIW DP K+HG +TLEGGDVMP+GNG+VL+GMGER+S Sbjct: 181 PETLLTAAIYRYHPKFAGKVHEIW-ADPLKNHGLATLEGGDVMPVGNGLVLVGMGERTSP 239 Query: 247 QAIGQVAQSLFAKGAAERVIVAGLPKSRAAMHLDTVFSFCDRDLVTVFPEVVKEIVPFSL 306 Q +G +AQ+LF +G A RVI +PKSRAAMHLDTVF+FC ++VT F EV E+ + L Sbjct: 240 QGVGLMAQALFGEGRATRVIACQMPKSRAAMHLDTVFTFCGDNIVTSFKEVADEMTCYDL 299 Query: 307 RPDPSSPYGMNIRREEKTFLEVVAESLGLKKLRVVETGGNS-FAAEREQWDDGNNVVCLE 365 P +++R + + EVVAE++G KKL VV TGG+ F REQW+DGNNV+ L Sbjct: 300 HPGEGDK-PLDMRHDTRPMFEVVAEAMGFKKLNVVPTGGSDPFEQSREQWNDGNNVLALR 358 Query: 366 PGVVVGYDRNTYTNTLLRKAGVEVITISASELGRGRGGGHCMTCPIVRDPI 416 PGVV+GYDRN TN LR G++VI + +ELGRGRGG CM+CP +RD + Sbjct: 359 PGVVMGYDRNDDTNAALRAEGIKVIELPGAELGRGRGGSRCMSCPTIRDAV 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: 544 Number of extensions: 14 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