Align proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_012102398.1 CKL_RS10110 FAD-dependent oxidoreductase
Query= BRENDA::Q76M76 (483 letters) >NCBI__GCF_000016505.1:WP_012102398.1 Length = 415 Score = 308 bits (789), Expect = 2e-88 Identities = 163/362 (45%), Positives = 242/362 (66%), Gaps = 9/362 (2%) Query: 120 DVVVIGGGPAGLMAAIHAADAGASVILIDENPMLGGQLVKQTHKFFGKREQFAGVRGVKI 179 D+V++G GPAGL A I A+ AGA V+++D N GGQL KQ HKFFG +GVRG+ I Sbjct: 45 DIVIVGAGPAGLAAGIEASLAGAEVLMVDLNMKPGGQLFKQIHKFFGSSAHRSGVRGMDI 104 Query: 180 AEILGEEVKKRGNIEVFLETSAVGVF---HEGEEKLVAAVRKNKELLEFLGKTLVVATGA 236 L ++ ++ G +E++L ++ +G+F G EK + ++L+ K +++A GA Sbjct: 105 GRELVKKAEENG-VEIWLGSTVIGLFPGNKVGIEK--GNDNEKRKLITVKAKKIIIAAGA 161 Query: 237 MEKMIPFENNDLPGIYGAGAIQTLMNTYGVKPGDRVLIVGAGNVGLILAYQLIQAGVEVK 296 E ++ F+ PG+ GAGA QT++N VKPG++V+++G+GNVGLI++YQL+QAG EV Sbjct: 162 SENVVRFKGWTKPGVMGAGAAQTMVNVNHVKPGEKVVMLGSGNVGLIVSYQLMQAGCEVV 221 Query: 297 AIVEAMPKVGGYFVHAAKVRRLGVPILTRHTILRAEGKDRVERAVIAQLDENWRPVPGTE 356 A+VEA PK+GGY VHAAK++R GVPI RHTI+ +G ++V VIA++DE +RP+ GTE Sbjct: 222 ALVEAAPKIGGYGVHAAKIKRAGVPIYIRHTIIEVKGDNKVCEVVIAEVDEKYRPIVGTE 281 Query: 357 KVFEVDTIALAVGLRPSIELLHQAGCQVKFVRELSGHVAVRDGRMETTVQGIFVAGDSAG 416 K+ + D +A+ VGL+PS+EL CQ F G V + + MET+ +GI+VAGD+ G Sbjct: 282 KIIKADVVAIGVGLKPSVELARLLKCQFTFNALFGGEVPLHNKDMETSNEGIYVAGDTTG 341 Query: 417 IEEATTAMLEGKIAGIAAALKAGAASPEWLAEIEKAQ--RDLLEFRSGPFGRHVLEGIKK 474 +EEA TA+ EG+IAGI+AA K G + +AE +K + + L R GPFG L ++ Sbjct: 342 VEEANTALEEGRIAGISAAQKLGYIDDD-IAENKKKEIWQRLKSLRLGPFGERRLRAKEQ 400 Query: 475 VL 476 ++ Sbjct: 401 IM 402 Lambda K H 0.319 0.138 0.397 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: 579 Number of extensions: 31 Number of successful extensions: 4 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: 483 Length of database: 415 Length adjustment: 33 Effective length of query: 450 Effective length of database: 382 Effective search space: 171900 Effective search space used: 171900 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 (21.8 bits) S2: 51 (24.3 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