Align proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_011841009.1 RSPH17029_RS07235 FAD-binding oxidoreductase
Query= BRENDA::Q8U022 (378 letters) >NCBI__GCF_000015985.1:WP_011841009.1 Length = 394 Score = 129 bits (323), Expect = 2e-34 Identities = 110/364 (30%), Positives = 164/364 (45%), Gaps = 24/364 (6%) Query: 4 IIGGGIIGVATAYELAKL--GEEVVVFEKR-YFGSGSTFRCASGIRAQFTDEANIKLMKY 60 +IGG ++G + AY L ++ G +V+V E+ + ST + IR QFT N+ + ++ Sbjct: 10 VIGGAVMGASAAYWLTRMQPGLKVIVVERDPTYARASTALSVASIRMQFTTPVNVAISRF 69 Query: 61 SIERWKTLSEELGHNIMFQ-----QTGYLFLATTEEEVEAFKKNIKLQNKFGVPTRLITP 115 I + E LG + + GYLFLA+T E + +Q G T ++TP Sbjct: 70 GIGFIREFRESLGQEVGIPSLGLTENGYLFLASTAEGASVLAEVAAMQRSLGAATEMLTP 129 Query: 116 EEAKEIVPPLNADAFLAGAWNPED-GKASPFHTLYAYKKAGERLGVKFYEYTKVVGIEK- 173 P L +AG++ P D G L ++ A GV+F VVG+E+ Sbjct: 130 AALAARFPWLETGDLVAGSFGPRDEGWFDNMGLLNGFRAAARLQGVEFLR-DGVVGLEQA 188 Query: 174 DGSKWKIKTTRGE-FKVDIIINATNAWAREINKMIGKDIIPVTPYKHQL-VKTEPIERGQ 231 G ++ GE INA+ A E+ +M G D +PV P K + V P R Sbjct: 189 QGRVRGVRLASGETIACGAAINASGTRAAEVMRMAGLD-LPVEPRKRTVFVIDAPNARHP 247 Query: 232 IEPLVCPPAWNDSYVIQDGEDGGVICGTALEYES--SPDDVTPTYEFVKEVL-KWAVKII 288 PL+ + + ++ G I T E +S P D P +EV+ + Sbjct: 248 DAPLLV----DRGFYLRPERGGQWITATVPETDSPCDPQDFEPDLHLFEEVVWEQLYARA 303 Query: 289 PALKHVHVVRQWAGHYA-KTPDKNPAIG--MIEENFYVAVGFSGHGFMMAPAVAQALAEK 345 P V VVR W GHYA D+N +G N Y+ GFSGHG APAV + +AE Sbjct: 304 PGFDAVKVVRHWVGHYAYNRLDQNAILGPHPALPNLYLMNGFSGHGLQQAPAVGRGIAEH 363 Query: 346 IVEG 349 ++ G Sbjct: 364 LLTG 367 Lambda K H 0.318 0.137 0.420 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: 308 Number of extensions: 15 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: 378 Length of database: 394 Length adjustment: 30 Effective length of query: 348 Effective length of database: 364 Effective search space: 126672 Effective search space used: 126672 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 Apr 10 2024. 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