Align proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_011880466.1 D-amino-acid oxidase
Query= BRENDA::Q76M73 (385 letters) >NCBI__GCF_000016205.1:WP_011880466.1 Length = 441 Score = 139 bits (350), Expect = 2e-37 Identities = 117/426 (27%), Positives = 185/426 (43%), Gaps = 66/426 (15%) Query: 3 SEAKTVIIGGGIIGLSIAYNLAKLGESDVVVLEKGYLGNGSTFRCGTGIRQQFNDEANIR 62 +EA V+IGGGIIG+ AY LA+ G S V ++EKG +G + R RQQ DE + Sbjct: 16 AEADVVVIGGGIIGVFTAYYLARRGVS-VALVEKGRIGAEQSSRNWGWCRQQNRDERELP 74 Query: 63 MMKRSVELWKGLSEELGMDVEFTQSGYLFLIYEKDELEAFKNNVRLQNRFGVPSRIITPE 122 M +S++LW+ + E G D F + G L+L ++ EL + + GV + ++ + Sbjct: 75 MASKSIDLWERFAAESGEDTGFHRCGLLYLSNDEAELSRWASWGEFAKTAGVTTYMLDSK 134 Query: 123 EAKEIVPPLNTNGVIAAAW-----NHTDGKANPFKAVFAYAEAAKRLGVEIYEYTEAKDI 177 +A E AW + +DG A+P KA A A A +LG ++++ A+ I Sbjct: 135 QAGE------RGRATGRAWKGGVFSPSDGTADPEKAAPAVAAALMKLGGSVHQHCAARGI 188 Query: 178 RVEEGKIKTVVTNRGEIKTGRVINAANAWAPLINKMAGVPIKIPIEPYKHQGVKTEPIK- 236 + G++ V+T G IKT +V+ A AWA + GV + P + + P++ Sbjct: 189 ELAAGRVAGVITEAGVIKTRKVVLAGGAWASSFCRQLGV--RFPQASIRQSILSVSPVEQ 246 Query: 237 --PG-------------------------QIEPMVISFKHGGVYLTQEAYQG-------- 261 PG +++P + ++ A + Sbjct: 247 ALPGALYTSGVSVTRRSDGRYALAISGRARVDPTAQFLRFAPQFVPMFAKRWRNLLPGGL 306 Query: 262 -GVIGGYG-LKY----GPT-------YDITPTYEFLRGVSYRFSQIIPALKYVNVIRIWG 308 GV GG+ LK PT D P + R +++P L+ + W Sbjct: 307 EGVRGGHETLKRWRLDAPTPMEAVRILDPKPDLPTVNETYRRAVELLPELRDATITHAWA 366 Query: 309 GFYAETPDHNAAIGRINEIDEFYIAAGFSGHGFMLAPAVAEALAEFIVDGKTDKPLDFYD 368 GF TPD IG + + +AAGFSGHGF + P +A+ + +PL Sbjct: 367 GFVDSTPDGVPGIGELPGVPGLVLAAGFSGHGFGIGPGAGHLIADLVTGA---QPLVDPT 423 Query: 369 PYRFER 374 PYR R Sbjct: 424 PYRPSR 429 Lambda K H 0.319 0.139 0.411 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: 415 Number of extensions: 22 Number of successful extensions: 3 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: 385 Length of database: 441 Length adjustment: 31 Effective length of query: 354 Effective length of database: 410 Effective search space: 145140 Effective search space used: 145140 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 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