Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized)
to candidate WP_012475433.1 CPHAMN1_RS10230 NAD-dependent succinate-semialdehyde dehydrogenase
Query= curated2:Q9K5Z5 (515 letters) >NCBI__GCF_000020545.1:WP_012475433.1 Length = 457 Score = 193 bits (490), Expect = 1e-53 Identities = 136/450 (30%), Positives = 210/450 (46%), Gaps = 26/450 (5%) Query: 52 IVSVNPAMKEQVIGVVSKASREIVDDAFKSAETAFHTWKNVNPEERANILIRAAAIIRRR 111 IV++NPA +E + S EI D +++E A WK + +ER + R A ++R + Sbjct: 2 IVTLNPANEEVLAEYPVMTSAEI-DRILEASENAALIWKKIPIDERKIAMHRLADLLREQ 60 Query: 112 KHEFSAWLVKEAGKPWKEADADTAEAIDFLEYYARQMITLKDGKPVNSREGEHNRYFYTP 171 K A + +E GK + E+ A+ + +YYA + V+ +G + P Sbjct: 61 KEMHGAMISREMGKRYAESVAEVEKCAWVCDYYAEHAEAFLQPEKVDM-DGGAGLVTFVP 119 Query: 172 IGVCVTISPWNFALAIMAGTTVAPIVTGNTVLLKPASTTPVVAAKFVEVLEEAGLPKGVV 231 +GV + + PWNF + A ++ GN V++K A A + EAG P V Sbjct: 120 LGVVLGVMPWNFPFWQVIRFAAAVMMAGNGVVIKHAPNVTGSAIALENLFREAGFP---V 176 Query: 232 NFVPGSGTDIGD------YLIDHPKTSLITFTGSRDVGVRLYERAAVVHPGQQHLKRVIV 285 N D+ D ++I HP ++ TGS GV + +A LKR ++ Sbjct: 177 NLYRTLHIDLEDVDRMVGHIIAHPVIKAVSVTGSTGAGVAVASKAGSA------LKRSVL 230 Query: 286 EMGGKDTVVVDKDADLDLAAQSIVTSAFGFSGQKCSAGSRAVIHQDVYDVVLEKAVALTK 345 E+GG D +V DADLD A + S +GQ C A R V+H+ V +K + Sbjct: 231 ELGGNDPYLVLDDADLDEAVGFCIASRLLNAGQSCIAAKRFVVHRSVTSRFEQKLLDTMS 290 Query: 346 QLSVGEPTAPDVYMGPVVDQGAFSKIMSYIEVGKEEG-RLMVGGEGDDSKGFFIQPTIFA 404 + VG+P P +++GP+ + + +E + G +++ GGE D KGFF PTI Sbjct: 291 KKKVGDPFDPGIHIGPIARKDLRDALHLQVEQSRGLGAKVLCGGEIPDRKGFFYPPTIVT 350 Query: 405 DVDPHARIMQEEIFGPVVAFSKARDFDHALEIANNTEYGLTGAVITTNRHHIEKAKRDFH 464 DV + EE FGPV +ARD D A+ IAN++ +GL AV + + + Sbjct: 351 DVSADMAVYSEETFGPVATILEARDDDDAVRIANDSPFGLGSAVFSGDPDRARRVAARLD 410 Query: 465 VGNLYFNRNCTGAIVGYH---PFGGFKMSG 491 GN C ++V PFGG K SG Sbjct: 411 AGNC-----CINSMVKSDPRLPFGGIKQSG 435 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: 520 Number of extensions: 27 Number of successful extensions: 5 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: 457 Length adjustment: 34 Effective length of query: 481 Effective length of database: 423 Effective search space: 203463 Effective search space used: 203463 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 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