Align proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_058930487.1 AU252_RS09435 sarcosine dehydrogenase
Query= BRENDA::O59089 (382 letters) >NCBI__GCF_001484605.1:WP_058930487.1 Length = 830 Score = 120 bits (301), Expect = 1e-31 Identities = 107/401 (26%), Positives = 175/401 (43%), Gaps = 43/401 (10%) Query: 8 IVVIGGGIVGVTIAHELAKRG-EEVTVIEKRFIG--SGSTFRCGTGIRQQFNDEANVRVM 64 IV+IG GIVG +A EL RG +TV+++ + GST + Q + Sbjct: 7 IVIIGAGIVGTNLADELVARGWNNITVLDQGPLNMPGGSTSHAPGLVFQTNPSKTMAAFA 66 Query: 65 KRSVELWKKYSEEYGFSFKQTGYLFLLYDDEEVKTFKRNIEIQNKFGVPTKLITPEEAKE 124 K +VE SE+ F Q G L + + + KR + +G+ K+++ EE KE Sbjct: 67 KYTVEKLLSLSEDGVSCFNQVGGLEVATTETRLADLKRKLGYAAAWGIDGKILSREECKE 126 Query: 125 IVPLLDISEVIAASWNPTDGKADPFEATTAFAVKAKEYGAKLLEYTEVKGFLIENNEIKG 184 + PL++ +++ P+DG A A + + G K + TEV G N + G Sbjct: 127 LYPLINEEDILGGLHVPSDGLAHAARAVQLLIKRTEAAGVKYIGNTEVTGIEQSNRRVTG 186 Query: 185 VKTNKGIIKTGIVVNATNAWANLINAMAGIKTKIPIEPYKHQAVITQPI---------KR 235 V+T +G+I IVV+ W I M G+ +P+ P HQ V T P+ Sbjct: 187 VETAEGVIPADIVVSCAGFWGAKIGEMIGM--SVPLLPLAHQYVKTTPVPAQQGKNELPN 244 Query: 236 GTINPMVISFKYGHAYLTQTFHGGIIGGIGYEIGP---------TYDLTPTYEFLREVSY 286 G P++ ++ L HG G Y P +Y+ + E Sbjct: 245 GASLPIL---RHQDQDLYYREHGERYGIGSYAHRPMPVDLDELGSYEPSSISEHNMPSRL 301 Query: 287 YFT------------KIIPALKNLLILRTWAGYYAKTPDSNPAIGRIEELNDYYIA-AGF 333 FT +++PAL+ I + G ++ TPD +G +E++ +Y+A A + Sbjct: 302 DFTLEDFLPAWEATKQLLPALRESEIEDGFNGIFSFTPDGGSLVGESKEVDGFYVAEAVW 361 Query: 334 SGHGFMMAPAVGEMVAELITKGKTKLPVEWYDPYRFERGEL 374 H + + VAEL+T GK+ + + D +RFE +L Sbjct: 362 VTH----SAGIARAVAELLTTGKSSIDLGDCDIHRFEDVQL 398 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: 662 Number of extensions: 35 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 382 Length of database: 830 Length adjustment: 36 Effective length of query: 346 Effective length of database: 794 Effective search space: 274724 Effective search space used: 274724 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: 53 (25.0 bits)
This GapMind analysis is from Sep 24 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