Align proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_011881407.1 (2Fe-2S)-binding protein
Query= BRENDA::Q76M76 (483 letters) >NCBI__GCF_000016205.1:WP_011881407.1 Length = 475 Score = 130 bits (326), Expect = 1e-34 Identities = 107/374 (28%), Positives = 158/374 (42%), Gaps = 54/374 (14%) Query: 122 VVIGGGPAGLMAAIHAADAGASVILIDENPMLGGQLVKQT---HKFFGKREQFAGVRGVK 178 V++G GPAG+ AA DAG ++IDEN GGQ+ +Q H F + G K Sbjct: 8 VIVGAGPAGVRAAEALVDAGLRPVVIDENARWGGQIYRQPPAGHAFTRGKRTLYGFDAAK 67 Query: 179 -------IAEILGEEVKKRGNIEVFLETSAVGVFHEGEEKLVAAVRKNKELLEFLGKTLV 231 +A +L + + T + +G E V R L+ Sbjct: 68 ADAVHRTMAALLPHVDYRPNTLAWACGTGRIDTLQDGREVTVPFSR------------LI 115 Query: 232 VATGAMEKMIPFENNDLPGIYGAGAIQTLMNTYGVKPGDRVLIVGAGNVGLILAYQLIQA 291 VA+GA ++M+P L G+Y G Q + G G RV+ G G + ++AYQ +A Sbjct: 116 VASGATDRMLPVPGWTLAGVYTLGGAQVALKAQGCAIGRRVVFAGTGPLLYLVAYQYAKA 175 Query: 292 GVEVKAIVEAMP------------------KVGGYFVHAAKVRRLGVPILTRHTILRAEG 333 G V A+++ P G Y++ +R GV + T T+ R G Sbjct: 176 GARVAAVLDTSPLRQQTAAAAALLRMPTTFAKGLYYI--GWLRAHGVAVETGVTLERVFG 233 Query: 334 KDRVERAVIAQLDENWRPVPGTEKVFEVDTIALAVGLRPSIELLHQAGCQVKFVRELSGH 393 V WR G + + D + L GLRP +L AGC+ +F Sbjct: 234 DQHVRGLA-------WRAADGDAHMLDCDALGLGFGLRPETQLADLAGCRFRFDPLSGAW 286 Query: 394 VAVRDGRMETTVQGIFVAGDSAGIEEATTAMLEGKIAGIAAALKAGAA--SPE---WLAE 448 + RD T+++G++VAGD AGI A A G+ A +A AG A SP A Sbjct: 287 LPERDAAGRTSMRGVYVAGDGAGIAGADAAEASGRRAALALLDDAGFAPGSPSGKPGAAA 346 Query: 449 IEKAQRDLLEFRSG 462 +E+ L FR+G Sbjct: 347 LERTLARLGAFRAG 360 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: 518 Number of extensions: 25 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: 1 Length of query: 483 Length of database: 475 Length adjustment: 34 Effective length of query: 449 Effective length of database: 441 Effective search space: 198009 Effective search space used: 198009 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: 51 (24.3 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