Align proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate GFF863 PGA1_c08760 sarcosine oxidase subunit alpha
Query= BRENDA::Q76M76 (483 letters) >FitnessBrowser__Phaeo:GFF863 Length = 973 Score = 131 bits (330), Expect = 9e-35 Identities = 138/496 (27%), Positives = 211/496 (42%), Gaps = 89/496 (17%) Query: 17 RKVTIHFEGQPVEAYEGETIAMALHAAGIRVLSHSAEKHRPRGLFCAIGKCSSCLVKVNG 76 R+V F G+ + EGE +A AL A I ++ S + HRPRG+ A + + LV V Sbjct: 13 REVGFSFNGRALTGREGEPLAAALLANNIHLVGRSFKYHRPRGILTAGSEEPNALVTVGE 72 Query: 77 ----VPNVRSCITLVEEGMKVEMQRG---------------------------------- 98 PN+R+ + EG+ Q Sbjct: 73 GAAQEPNLRATTLPLYEGLAARSQNCWPSVGFDVMAVNDLAAPFLGAGFYYKTFMWPAAF 132 Query: 99 ---------KETLPKGAKPPAWKDAPRYKA----DVVVIGGGPAGLMAAIHAADAGASVI 145 + GA A D KA D++VIG GPAGLMAA+ AA GA VI Sbjct: 133 WEKIYEPVIRRAAGLGALSGAPDDGIYEKAYGFCDLLVIGAGPAGLMAALTAARGGADVI 192 Query: 146 LIDENPMLGGQLVKQTHKFFGKREQFAGVRGVKIAEILGEEVKKRGNIEVFLETSAVGVF 205 L DE+ GG+L+ + G Q +A L E + N+ TS GV+ Sbjct: 193 LCDEDSQPGGRLLSEQETINGNPAQ------QWVAATLAE-LDSLNNVRRMARTSVTGVY 245 Query: 206 HEGE----EKLVAAVRKNKELL--EFLGKTLVVATGAMEKMIPFENNDLPGIYGAGAIQT 259 +G E + A K + K ++A GA+E+ + F NND PGI AGA+++ Sbjct: 246 DQGTYGALETVPAGGGKPARACFWRLVAKRAILAAGALERPVAFANNDRPGIMLAGAVRS 305 Query: 260 LMNTYGVKPGDRVLIVGAGNVGLILAYQLIQAGVEVKAIVEAMPKVGGYFVHAAKVRRLG 319 +N +GV PG+RV + + A L+ AGV V A++++ H A + Sbjct: 306 YLNRWGVAPGERVTVFANNDDAHRTARDLLAAGVHVAAVIDSR--------HDAP-QSDA 356 Query: 320 VPILTRHTILRAEGKDRVERAVIAQLDENWRPVPGTEKVFEVDTIALAVGLRPSIELLHQ 379 ++ + A G+ R+E + R V G EK+ + D +A++ G P++ L Sbjct: 357 FRVIRGAQVCNASGRQRLESLTL-------RSVSGEEKL-QTDCLAMSGGWNPTLHLTCH 408 Query: 380 AGCQVKFVRELSGHVAVRDGRMETTVQGIFVAGDSAGIEEATTAMLEGKIAGIAA--ALK 437 + ++ R+L+ V +DG V G+ G G + +G AG A AL Sbjct: 409 LNGRPRWRRDLACFVP-QDG----AVPGLEAVGACRGRFTTMAVLQDGAEAGARALEALG 463 Query: 438 AGAASPEWLAEIEKAQ 453 A + E L E E+A+ Sbjct: 464 KRAVAAE-LPEAEQAE 478 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: 1043 Number of extensions: 58 Number of successful extensions: 4 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: 973 Length adjustment: 39 Effective length of query: 444 Effective length of database: 934 Effective search space: 414696 Effective search space used: 414696 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 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