Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized)
to candidate WP_011373513.1 SUDEN_RS09855 aldehyde dehydrogenase family protein
Query= curated2:Q9K5Z5 (515 letters) >NCBI__GCF_000012965.1:WP_011373513.1 Length = 471 Score = 190 bits (483), Expect = 8e-53 Identities = 130/425 (30%), Positives = 212/425 (49%), Gaps = 22/425 (5%) Query: 76 DDAFKSAETAFHTWKNVNPE---ERANILIRAAAIIRRRKHEFSAWLVKEAGKPWKEADA 132 DDA K+ A K + +R + L+ A+ + + K + + + E GKP + Sbjct: 38 DDAKKALNIALLASKEASKTTIAQRCSWLLDVASKLAQNKEDIAKTITDEVGKPITYSRI 97 Query: 133 DTAEAIDFLEYYARQMITLKDGKPVNS---REGEHNRYFYT--PIGVCVTISPWNFALAI 187 + I+ + A M T+ G+ VN+ G+ F++ P GV V I+P+NF L + Sbjct: 98 EVERCIETVTLAAETMRTMH-GETVNTDAFASGKKTISFFSRVPCGVVVAITPFNFPLNL 156 Query: 188 MAGTTVAPIVTGNTVLLKPASTTPVVAAKFVEVLEEAGLP-KGVVNFVPGSGTDIGDYLI 246 +A +V GN V+LKP P+ A KF ++ E+ K ++ V G D+G L+ Sbjct: 157 IAHKIAPALVAGNAVILKPTPEAPLTAYKFAKLFIESEFAIKDALSVVYGDA-DVGGTLV 215 Query: 247 DHPKTSLITFTGSRDVGVRLYERAAVVHPGQQHLKRVIVEMGGKDTVVVDKDADLDLAAQ 306 +I+FTGS VG + + A + K+V +E+GG +DK A+LDLAAQ Sbjct: 216 TSEIPRVISFTGSVGVGEIITKSAGI--------KKVSLELGGNAATFIDKSANLDLAAQ 267 Query: 307 SIVTSAFGFSGQKCSAGSRAVIHQDVYDVVLEKAVALTKQLSVGEPTAPDVYMGPVVDQG 366 AF SGQ C + R +H+D+Y K TK+L VG P D +MGP+V+ Sbjct: 268 RCAIGAFVNSGQVCISLQRIYVHKDIYSEFALKIAEATKKLVVGSPYEEDTFMGPLVNDE 327 Query: 367 AFSKIMSYIEVGKEEGRLMVGGEGDDSKGFFIQPTIFADVDPHARIMQEEIFGPVVAFSK 426 A + M +++ +EG + + + F+ P + ADV I+ +E+F P+V+ + Sbjct: 328 AAKRAMEWVQSAIKEGATPILEPRVEGRVFY--PCVMADVKEDMAIVCQEVFAPIVSLIE 385 Query: 427 ARDFDHALEIANNTEYGLTGAVITTNRHHIEKAKRDFHVGNLYFNRNCTGAIVGYHPFGG 486 +DFD AL + NN+ YGL ++ T + + ++A + G + N T P+GG Sbjct: 386 VKDFDEALPMMNNSPYGLQFSIFTNDLNLTKRAINELDAGGIVINDMPT-LRFDIQPYGG 444 Query: 487 FKMSG 491 K+SG Sbjct: 445 VKLSG 449 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: 508 Number of extensions: 26 Number of successful extensions: 4 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: 471 Length adjustment: 34 Effective length of query: 481 Effective length of database: 437 Effective search space: 210197 Effective search space used: 210197 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 Apr 09 2024. 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