Align proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_068463362.1 APY04_RS13045 aminomethyltransferase
Query= BRENDA::Q76M76 (483 letters) >NCBI__GCF_001541235.1:WP_068463362.1 Length = 976 Score = 178 bits (452), Expect = 7e-49 Identities = 148/465 (31%), Positives = 221/465 (47%), Gaps = 71/465 (15%) Query: 23 FEGQPVEAYEGETIAMALHAAGIRVLSHSAEKHRPRGLFCAIGKCSSCLVKVNGVPNVRS 82 F+G+ Y G+ IA AL+A G R+LS S + HRPRG G ++ +V+V PNVR+ Sbjct: 31 FDGKLHMGYAGDVIASALYAGGQRLLSRSFKYHRPRGALTMSGHDANTIVQVADEPNVRA 90 Query: 83 CITLVEEGMKVE---------------MQRGKETLPKG---------------------- 105 + +G+ V M K LP G Sbjct: 91 DRYNLRDGISVASVNRLGSLNFDMLAVMGAFKRFLPVGFYYKTFFRPKGIWPWFEKPIRH 150 Query: 106 ----------AKPPAWKDAPRYKADVVVIGGGPAGLMAAIHAADAGASVILIDENPMLGG 155 AKP ++ A ++ ADV+V+GGG AG+ AA+ AA++GA +LIDE LGG Sbjct: 151 MAGLGYLEPAAKPRSYDKAYKF-ADVLVVGGGAAGIEAALAAAESGAETLLIDEWAELGG 209 Query: 156 QLVKQTHKFFGKREQFAGVRGVKIAEILGEEVKKRGNIEVFLETSAVGVFHEGEEKLVAA 215 L+ +G+ E G+ E+L V++ N++V T+ GVF + + A Sbjct: 210 SLL------YGRGEFSRGLTDEVRRELLAR-VQQAENLQVMTGTTVSGVFADNWVSALDA 262 Query: 216 VRKNKELLEFLGKTLVVATGAMEKMIPFENNDLPGIYGAGAIQTLMNTYGVKPGDRVLIV 275 K L + K +V+ATGA E+ + F NND PGI A A Q LM YGV P +R +I Sbjct: 263 ----KRLYKIRAKQIVLATGAFEQPLVFPNNDRPGIMFASAAQRLMRLYGVCPANRAVIA 318 Query: 276 GAGNVGLILAYQLIQAGVEVKAIVE--AMPKVGGYFVHAAKVRRLGVPILTRHTILRAEG 333 + G A L+ AG V A+V+ A P+ G + VR GV +LT + ++G Sbjct: 319 TSNRFGYEAALDLLDAGASVAAVVDLRAKPEAG---MAEDAVRARGVRVLTGAMPVNSKG 375 Query: 334 KDRVERAVIAQLDENWRPVPGTEKVFEVDTIALAVGLRPSIELLHQAGCQVKFVRELSGH 393 + + IA++ ++ + GT + + D + +AVG P + L AG + + E + Sbjct: 376 RRGITGVAIARIADDGK-TTGTAQWIDCDGLLMAVGFAPQLNLACHAGARAVYDAETNMQ 434 Query: 394 VAVRDGRMETTVQGIFVAGDSAGIEEATTAMLEGKIAGIAAALKA 438 R E GI +AG +AG +AT A G AG AA +A Sbjct: 435 ------RAEGVPDGITLAGCAAGHWDATDARAGGAAAGKRAAARA 473 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: 1005 Number of extensions: 48 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: 976 Length adjustment: 39 Effective length of query: 444 Effective length of database: 937 Effective search space: 416028 Effective search space used: 416028 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