Align proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate H281DRAFT_02458 H281DRAFT_02458 sarcosine oxidase subunit alpha
Query= BRENDA::Q76M76 (483 letters) >FitnessBrowser__Burk376:H281DRAFT_02458 Length = 1000 Score = 139 bits (351), Expect = 3e-37 Identities = 139/506 (27%), Positives = 219/506 (43%), Gaps = 79/506 (15%) Query: 15 RGRKVTIHFEGQPVEAYEGETIAMALHAAGIRVLSHSAEKHRPRGLFCAIGKCSSCLVKV 74 R +T F G+ + Y+G+T+A AL A G+ ++ S + HRPRG+ A + + +V++ Sbjct: 15 RALPLTFTFNGRQYQGYQGDTLASALLANGLHFVARSWKYHRPRGIVTAGVEEPNAVVQL 74 Query: 75 NG----VPNVRSCITLVEEGMKVEMQRGKETLPKG------------------------- 105 VPN R+ + +G+ K ++ K Sbjct: 75 ETGAYTVPNARATEVELYQGLVANSVNAKPSIEKDRMAVNQKLARFIPAGFYYKTFMWPR 134 Query: 106 ----------------AKPPAWKDAPRYK-----ADVVVIGGGPAGLMAAIHAADAGASV 144 K P DA RY DV+V+GGGP GL AA AA +GA V Sbjct: 135 KFWPKYEEVIRDAAGLGKAPEQLDADRYDKCFAHCDVLVVGGGPTGLAAAHAAALSGARV 194 Query: 145 ILIDENPMLGGQLVKQTHKFFGKREQFAGVRGVKIAEILGEEVKKRGNIEVFLETSAVG- 203 L+D+ P LGG L+ R + G ++ + +E+++ ++++ ++A G Sbjct: 195 TLVDDQPELGGSLLSC-------RAEIDGKPALQWVHKIEDELRQMPDVKILTRSTAFGY 247 Query: 204 -------VFHEGEEKLVAAVRKN-KELL-EFLGKTLVVATGAMEKMIPFENNDLPGIYGA 254 V + L + RK +EL+ + K +++ATGA E+ I F NNDLPG+ A Sbjct: 248 QDHNLVTVTQRLTDHLPVSQRKGTRELMWKIRAKRVILATGAHERPIVFGNNDLPGVMLA 307 Query: 255 GAIQTLMNTYGVKPGDRVLIVGAGNVGLILAYQLIQAGVEVKAIVEAMPKVGGYFVHAAK 314 A+ T ++ Y V PG ++ + G A L AG +V I + G A Sbjct: 308 SAVSTYLHRYAVLPGRNAVVFTNNDDGYQCALDLKAAGAQVTVIDPRAGESKGTL--PAL 365 Query: 315 VRRLGVPILTRHTILRAEGKDRVERAVIAQLDENWRPVPGTEKVFEVDTIALAVGLRPSI 374 RR GV ++ I A GK RV IA +E D +A++ G P + Sbjct: 366 ARRYGVKVIGGAVITAAHGKLRVASVDIASYANGKTGAKQSE--LPCDLLAMSGGWSPVL 423 Query: 375 ELLHQAGCQVKFVRELSGHVAVRDGRMETTV---QGIFVAGDSAGIEEATTAMLEGKIAG 431 L Q+G + + E + V + + ET+V G F G GI A A +E A Sbjct: 424 HLFAQSGGKAHWHNEKACFVPGKAMQAETSVGACNGDFTLGQ--GIRFAVDAGIE---AA 478 Query: 432 IAAALKAGAASPEWLAEIEKAQRDLL 457 AA +P +AEI +A+ + L Sbjct: 479 RAAGHIVARPNPVQVAEISEAKLEPL 504 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: 1054 Number of extensions: 68 Number of successful extensions: 5 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: 1000 Length adjustment: 39 Effective length of query: 444 Effective length of database: 961 Effective search space: 426684 Effective search space used: 426684 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