Align D-arginine dehydrogenase (EC 1.4.99.6) (characterized)
to candidate HSERO_RS11185 HSERO_RS11185 amino acid dehydrogenase
Query= BRENDA::Q9HTQ0 (432 letters) >FitnessBrowser__HerbieS:HSERO_RS11185 Length = 423 Score = 226 bits (576), Expect = 1e-63 Identities = 146/417 (35%), Positives = 215/417 (51%), Gaps = 14/417 (3%) Query: 2 RVLVLGSGVIGTASAYYLARAGFEVVVVDRQDGPALETSFANAGQVSPGYASPWAAPGIP 61 ++ V+G G+ G SAY+LA G+EV V++R+ A E +F ++G ++PG A P PG Sbjct: 7 QIAVIGGGLSGICSAYFLATKGYEVAVIERRAHVAEEATFGDSGLLAPGTAMPLTLPGA- 65 Query: 62 LKAMKWLLEKHAPLAIKLTSDPSQYAWMLQMLRNCTAERYAVNKERMVRLSEYSRDCLDE 121 L + + + +D + WM + R +A +K + RLS Y +D + Sbjct: 66 LATFACRFQDEPRVLLASGADFGRRRWM-RATRAAQQHHFAQHKLILSRLSAYGQDLTQQ 124 Query: 122 LRAETGIAYEGRTLGTTQLFRTQAQLDAAGKDIAVLERSGVPYE--VLDRDGIARVEPAL 179 L+A + +E + G LFR A+ AA S Y+ LD GI +EPA Sbjct: 125 LQAHYNMEHEN-SAGVFHLFRQSAE--AARLPALQEAASQCEYKQLTLDAAGIRALEPAF 181 Query: 180 AKVADKLVGALRLPNDQTGDCQLFTTRLAEMAKGLGVEFRFGQNIE--RLDFAGDRINGV 237 + A L GAL P+D G+ LF ++ A+ LGV F F + R +F G R+ Sbjct: 182 SSEA-ALAGALYYPDDIAGNSVLFAKQMRNAAQALGVSFHFNSTVSSIRSEFGG-RVTLE 239 Query: 238 LVNGEL---LTADHYVLALGSYSPQLLKPLGIKAPVYPLKGYSLTVPITNPEMAPTSTIL 294 + + L LT D V+A G S LL+PL P+ L+ YS VP+ NP+ APT + Sbjct: 240 VQSPHLASHLTMDAVVVAAGMASAALLQPLDTSLPLRALQSYSALVPVKNPDDAPTMALY 299 Query: 295 DETYKVAITRFDQRIRVGGMAEIAGFDLSLNPRRRETLEMITTDLYPEGGDISQATFWTG 354 D++YKVA+TR RIR+ G+ +L P+ L I D YP + +QA FW+ Sbjct: 300 DDSYKVAMTRLGSRIRISGLLGFVPASQTLPPKALRNLLKIAGDYYPNAANYNQAHFWSN 359 Query: 355 LRPATPDGTPIVGATRYRNLFLNTGHGTLGWTMACGSGRYLADLMAKKRPQISTEGL 411 P G P+VG TR N+F+N GHG GW + GS R L+D+MA + +I+T GL Sbjct: 360 SIAMMPTGLPVVGPTRQGNIFVNVGHGVTGWAASVGSARLLSDMMAGEETEIATAGL 416 Lambda K H 0.318 0.135 0.401 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: 366 Number of extensions: 16 Number of successful extensions: 3 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: 432 Length of database: 423 Length adjustment: 32 Effective length of query: 400 Effective length of database: 391 Effective search space: 156400 Effective search space used: 156400 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: 51 (24.3 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