Align proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate BPHYT_RS29290 BPHYT_RS29290 D-amino acid oxidase
Query= BRENDA::Q5JFG7 (386 letters) >FitnessBrowser__BFirm:BPHYT_RS29290 Length = 441 Score = 144 bits (362), Expect = 6e-39 Identities = 115/423 (27%), Positives = 181/423 (42%), Gaps = 61/423 (14%) Query: 6 LPEKSEITIIGGGIVGVTIAHELAKRGEEVTVIEKRFIGSGSTFRCGTGIRQQFNDEANV 65 LP +++ +IGGGI+GV A+ +A+RG V ++EK IG+ + R RQQ DE + Sbjct: 14 LPAAADVVVIGGGIIGVFAAYYMAQRGVSVALVEKGRIGAEQSSRNWGWCRQQNRDEREL 73 Query: 66 QVMKRSVELWKKYSEEYG--FPFQQTGYLFLLYDDEEVETFKRNIAIQNKFGVPTRLITP 123 + +S++LW++++ E G F + G L+L DD E+ + GV T L+ Sbjct: 74 PIASKSLDLWERFAVESGEDTGFHRCGLLYLSNDDAELARWASWGDFAKTAGVTTYLLDS 133 Query: 124 EEAKEIVPLLDISEVVAASW-----NPTDGKASPFHSTAKFALHAEEFGAKLVEYTEVKD 178 ++A E + +W +P+DG A P + A + G + + + Sbjct: 134 KQAAE------RGKATGRAWKGGVFSPSDGTADPAKAAPAVATALMKLGGSVTQQCAARG 187 Query: 179 FIIENGEIKGLKTSRGTIKTGIVVNATNAWAKLINAMAGIR-----------TKIPIEPY 227 +E G + G+ T G IKT VV A AWA GIR + P+E Sbjct: 188 IELEGGRVCGVVTEAGVIKTRTVVLAGGAWASAFCRQLGIRFPQASIRQSILSVSPVETP 247 Query: 228 KHQAVITQPIK-----------------KGSVKPMVISF--RYGHAYLTQTSH---GGII 265 A+ T + + V P + F ++ + + + GG+ Sbjct: 248 LPDALFTSGVSITRRTDGRYALAISGRARVDVTPQFLRFAPQFVPMFAKRWRNLLPGGLE 307 Query: 266 GGVGYEE--------GPT-------YDLNPTYEFLREVSYYFTKIIPALRELLILRTWAG 310 G G E PT D P +RE +++P L + I WAG Sbjct: 308 GVRGGHETLKRWQLDAPTPMERVRILDPKPDMPTVRETHRRAIELLPELGKAKITHAWAG 367 Query: 311 YYAKTPDSNPAIGKIEELSDYYIAAGFSGHGFMMAPAVAEMVADLITKGKTDLPAWWYDP 370 + TPD P IG++ + +AAGFSGHGF + P ++ADL T + Y P Sbjct: 368 FVDSTPDGVPGIGEVPGVPGLILAAGFSGHGFGIGPGAGHLIADLATGAAPIVDPIPYRP 427 Query: 371 YRF 373 RF Sbjct: 428 ARF 430 Lambda K H 0.318 0.137 0.406 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: 395 Number of extensions: 19 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: 386 Length of database: 441 Length adjustment: 31 Effective length of query: 355 Effective length of database: 410 Effective search space: 145550 Effective search space used: 145550 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