Align proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_015934208.1 MNOD_RS37755 sarcosine oxidase subunit alpha
Query= BRENDA::Q76M76 (483 letters) >NCBI__GCF_000022085.1:WP_015934208.1 Length = 999 Score = 147 bits (372), Expect = 1e-39 Identities = 132/491 (26%), Positives = 207/491 (42%), Gaps = 85/491 (17%) Query: 17 RKVTIHFEGQPVEAYEGETIAMALHAAGIRVLSHSAEKHRPRGLFCAIGKCSSCLVKVNG 76 R + F+G+ + G+T+A AL A G+ ++ S + HRPRG+ A + L+ + Sbjct: 16 RPIRFSFDGKDYQGLAGDTLASALLANGVHLIGRSFKYHRPRGVVSAGSDEPNALLGTHR 75 Query: 77 -----VPNVRSCITLVEEGMKVEMQ----------------------------------- 96 PN R+ I + +G+ Q Sbjct: 76 GPGRFEPNTRATIQELRDGLVATSQNRWPSLAFDVGSINDRLGSLFSAGFYYKTFMWPRA 135 Query: 97 ---RGKETLPKGAK----PPAWKDAPRYKA-----DVVVIGGGPAGLMAAIHAADAGASV 144 R E + + A P DA RY + DV+++G GPAGL AA+ A +GASV Sbjct: 136 FWDRVYEPVIRNAAGLGVSPTEPDADRYASRFAHTDVLIVGAGPAGLAAALAAGRSGASV 195 Query: 145 ILIDENPMLGGQLVKQTHKFFGKREQFAGVRGVKIAEILGE---EVKKRGNIEVFLETSA 201 +L+DE GG L+ E + G + L E+ N+ V T+A Sbjct: 196 MLVDETAEPGGSLLS---------EPAVAIDGKPAWDWLAATLAELAALPNVTVMTRTTA 246 Query: 202 VGVFHEG--------EEKLVA--AVRKNKELLEFLGKTLVVATGAMEKMIPFENNDLPGI 251 +G +H+ + L A A + L + +V+A GA+EK + F+ ND PG+ Sbjct: 247 IGYYHQNLVGLAQRLTDHLAAPPADAPRERLWKVRAGQVVLAQGALEKPLVFDGNDRPGV 306 Query: 252 YGAGAIQTLMNTYGVKPGDRVLIVGAGNVGLILAYQLIQAGVEVKAIVEAMPKVGGYFVH 311 AGA QT +N YGV+ GDR IV A + A+ L +AG + AIV+ P V Sbjct: 307 MLAGAAQTYLNRYGVRVGDRTAIVTAHDSAWYAAFDLAEAGAKPVAIVDIRPIVD--LAL 364 Query: 312 AAKVRRLGVPILTRHTILRAEGKDRVERAVIAQLDENWRPVPGTEKVFEVDTIALAVGLR 371 K R LG+ +L HT+ EG+ RV+ + + G + D + + G Sbjct: 365 TDKARALGIELLLGHTVTGTEGRLRVKSLRVNPVRNG---KAGAARRIACDAVLMCGGWT 421 Query: 372 PSIELLHQAGCQVKFVRELSGHVAVRDGRMETTVQGIFVAGDSAGIEEATTAMLEGKIAG 431 P + L + + L +A + + + +AG G+ A+ +G AG Sbjct: 422 PCLHLFSHTKGSLAWDETLQAFLA------DKKSEAVHIAGAGRGLWGIAAALTDGAAAG 475 Query: 432 IAAALKAGAAS 442 AA AG A+ Sbjct: 476 ARAARDAGRAA 486 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: 1019 Number of extensions: 53 Number of successful extensions: 6 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: 483 Length of database: 999 Length adjustment: 39 Effective length of query: 444 Effective length of database: 960 Effective search space: 426240 Effective search space used: 426240 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: 54 (25.4 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