Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized)
to candidate CCNA_02480 CCNA_02480 NAD-dependent benzaldehyde dehydrogenase II
Query= curated2:Q9K5Z5 (515 letters) >FitnessBrowser__Caulo:CCNA_02480 Length = 487 Score = 228 bits (582), Expect = 3e-64 Identities = 144/451 (31%), Positives = 226/451 (50%), Gaps = 16/451 (3%) Query: 52 IVSVNPAMKEQVIGVVSKASREIVDDAFKSAETAFHTWKNVNPEERANILIRAAAIIRRR 111 +++V E V+ V +A R V A SA+ A W + + R IL+RAA ++ Sbjct: 27 VIAVQEPATETVLTQVGRADRSDVARAAASAKAAQPAWAALTADARQAILLRAADLLVEH 86 Query: 112 KHEFSAWLVKEAGKPWKEADADTAEAIDFLEYYARQMITLKDGKPVNSREGEHNRYFYTP 171 + + W+++E+G +A + A F+ A M T G + S G+ + P Sbjct: 87 APDLAPWIMRESGSVAAKAAVELEHAAGFVRQ-AGAMATEAAGLVLPSSPGKTSIARRVP 145 Query: 172 IGVCVTISPWNFALAIMAGTTVAPIVTGNTVLLKPASTTPVVAAKFV-EVLEEAGLPKGV 230 +GV ISP+NF L + + TGN V+LKP TP+ + V E AGLP G+ Sbjct: 146 LGVVAVISPFNFPLVLSIRAVAPALATGNAVVLKPDPRTPISGGFLIARVFEAAGLPAGL 205 Query: 231 VNFVPGSGTDIGDYLIDHPKTSLITFTGSRDVGVRLYERAAVVHPGQQHLKRVIVEMGGK 290 ++ +PG + GD L P +++ FTGS G ++ E A HLK+V +E+GGK Sbjct: 206 LHVLPGDA-EAGDALCRDPNIAMVAFTGSTGAGRKVGEVAGA------HLKKVALELGGK 258 Query: 291 DTVVVDKDADLDLAAQSIVTSAFGFSGQKCSAGSRAVIHQDVYDVVLEKAVALTKQLSVG 350 + +++ DAD D+AA + A+ GQ C R ++ + ++D V+E+ A L VG Sbjct: 259 NPLIILDDADPDVAASNAAWGAWLHQGQVCMTAGRLLVQRGIHDAVVERLAAKAGHLPVG 318 Query: 351 EPTAPDVYMGPVVDQGAFSKIMSYIEVGKEEG-RLMVGGEGDDSKGFFIQPTIFADVDPH 409 +P DV +GP++ +G ++ + + +G RL+ GG KG PT+ V P Sbjct: 319 DPMRGDVALGPLISRGQLDRVHAIVSDTVADGARLVAGG---THKGLCYAPTVLTGVAPG 375 Query: 410 ARIMQEEIFGPVVAFSKARDFDHALEIANNTEYGLTGAVITTNRHHIEKAKRDFHVGNLY 469 R +EEIFGP+ A + D D A +AN+ YGL+ +I+ + VG+L+ Sbjct: 376 MRAFEEEIFGPIAAVTVFDDLDEAARLANDGPYGLSAGIISGSVGRAMTLGAKLEVGHLH 435 Query: 470 FNRNCTGAIVGYH-PFGGFKMSGTDSKAGGP 499 N A G H PFGG K SG ++ GP Sbjct: 436 INDQTVDA--GPHSPFGGMKASGNGTRISGP 464 Lambda K H 0.318 0.135 0.394 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: 606 Number of extensions: 27 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 515 Length of database: 487 Length adjustment: 34 Effective length of query: 481 Effective length of database: 453 Effective search space: 217893 Effective search space used: 217893 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 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