Align proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate HSERO_RS05695 HSERO_RS05695 D-amino acid oxidase
Query= BRENDA::O59089 (382 letters) >FitnessBrowser__HerbieS:HSERO_RS05695 Length = 441 Score = 154 bits (389), Expect = 5e-42 Identities = 117/422 (27%), Positives = 186/422 (44%), Gaps = 61/422 (14%) Query: 3 PEKSEIVVIGGGIVGVTIAHELAKRGEEVTVIEKRFIGSGSTFRCGTGIRQQFNDEANVR 62 P +++VVIGGGI+G+ A+ LAKRG V V+EK IG+ + R RQQ D + Sbjct: 15 PASADVVVIGGGIIGIFTAYFLAKRGISVAVVEKGRIGAEQSSRNWGWCRQQNRDARELP 74 Query: 63 VMKRSVELWKKYSEEYG--FSFKQTGYLFLLYDDEEVKTFKRNIEIQNKFGVPTKLITPE 120 + +S++LW+++S E G F + G L+L D+EE+ + + GV T ++ + Sbjct: 75 MATKSIDLWEQFSAETGEDTGFNRCGLLYLSNDEEEIARWAAWGDFAKTAGVTTYMLDSK 134 Query: 121 EAKEIVPLLDISEVIAASW-----NPTDGKADPFEATTAFAVKAKEYGAKLLEYTEVKGF 175 +A E +W +PTDG ADP +A A A + G +++ +G Sbjct: 135 QAAE------RGHATGRAWKGGVFSPTDGTADPGKAAPAVARAIMKLGGHVIQQCAARGI 188 Query: 176 LIENNEIKGVKTNKGIIKTGIVVNATNAWANLINAMAGIK-----------TKIPIEPYK 224 E + GV T G+IKT + V A AWA+ GI+ + P+E Sbjct: 189 DTEGGRVSGVITEAGVIKTKVAVMAGGAWASSFCHQLGIRFPQASVRQSIMSVAPMEAPL 248 Query: 225 HQAVITQPIK---------------RGTINPMVISFKYGHAYL---TQTFHGGIIGGI-- 264 A+ T + R ++P + ++ +L + + GG+ Sbjct: 249 PGALYTSGVAVTRRSDGSYALAISGRARVDPTMQFLRFSPQFLPMFAKRWRSLSPGGLEA 308 Query: 265 ---GYEI-------GPT-------YDLTPTYEFLREVSYYFTKIIPALKNLLILRTWAGY 307 G+E PT D + +R +++P L + TWAGY Sbjct: 309 WRSGHETLSRWRMDAPTPMERMRILDASADPASIRATHRRAVELLPQLAQAKVTHTWAGY 368 Query: 308 YAKTPDSNPAIGRIEELNDYYIAAGFSGHGFMMAPAVGEMVAELITKGKTKLPVEWYDPY 367 TPD P IG + + +AAGFSGHGF + P G ++A+L + + Y P Sbjct: 369 VDSTPDGVPGIGELPQTPGLILAAGFSGHGFGIGPGAGHLIADLASGAAPIVDPRPYHPN 428 Query: 368 RF 369 RF Sbjct: 429 RF 430 Lambda K H 0.318 0.138 0.405 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: 365 Number of extensions: 14 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 382 Length of database: 441 Length adjustment: 31 Effective length of query: 351 Effective length of database: 410 Effective search space: 143910 Effective search space used: 143910 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: 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