Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized)
to candidate WP_012536996.1 AFE_RS09825 aldehyde dehydrogenase family protein
Query= curated2:Q9K5Z5 (515 letters) >NCBI__GCF_000021485.1:WP_012536996.1 Length = 506 Score = 189 bits (479), Expect = 3e-52 Identities = 132/438 (30%), Positives = 213/438 (48%), Gaps = 25/438 (5%) Query: 67 VSKASREIVDDAFKSAETAFHTWKNVNPEERANILIRAAAIIRRRKHEFSAWLVKEAGKP 126 + ++S E ++ A +A A W + R+NIL++ A I + + GK Sbjct: 50 IPRSSAEDIELALDAAHAAKDAWGRTSVTARSNILLKIADRIDANLEMLAVAETWDNGKA 109 Query: 127 WKEA-DADTAEAIDFLEYYARQMITLKDGKPVNSREGEHNRYFYTPIGVCVTISPWNFAL 185 +E +AD + D Y+A + ++G E +F+ P+GV I PWNF L Sbjct: 110 VRETLNADVPLSSDHFRYFAG-CLRAQEGTIGEIDENTVAYHFHEPLGVVGQIIPWNFPL 168 Query: 186 AIMAGTTVAPIVTGNTVLLKPASTTPVVAAKFVEVLEEAGLPKGVVNFVPGSGTDIGDYL 245 + + GN V+LKPA TP +E++ + LP GV+N V G G + G L Sbjct: 169 LMACWKLAPALAAGNCVVLKPAEQTPASILVMMELIADL-LPAGVLNVVNGYGVEAGKAL 227 Query: 246 IDHPKTSLITFTGSRDVGVRLYERAAVVHPGQQHLKRVIVEMGGKDT------VVVDKDA 299 + + I FTGS VG + + AA +++ VE+GGK V+ +DA Sbjct: 228 ATSKRIAKIAFTGSTPVGSLIMKYAA------ENIIPSTVELGGKSPNIFFADVLDQEDA 281 Query: 300 DLDLAAQSIVTSAFGFSGQKCSAGSRAVIHQDVYDVVLEKAVALTKQLSVGEPTAPDVYM 359 + A + V + F G+ C+ SR +I + +Y+ + V + Q+ G P +V + Sbjct: 282 FVSKAVEGAVLAFFN-QGEVCTCPSRLLIQESIYEKFIGMVVERSAQIKRGNPLDTEVMV 340 Query: 360 GPVVDQGAFSKIMSYIEVGKEEGRLMVGG------EGDDSKGFFIQPTIFADVDPHARIM 413 G Q + KI+SYI++GK+EG ++ G D +G++IQPT+ + + R+ Sbjct: 341 GAQASQEQYDKILSYIQIGKDEGAEVITGGAVETMSADYCEGYYIQPTLLKGTN-NMRVF 399 Query: 414 QEEIFGPVVAFSKARDFDHALEIANNTEYGLTGAVITTNRHHIEKAKRDFHVGNLYFNRN 473 QEEIFGPVV+ + +D AL IAN+ E+GL V T + + + R G ++ N Sbjct: 400 QEEIFGPVVSVTTFKDEAEALAIANDIEFGLGAGVWTRDMNRAYRMGRGIQAGRVW--TN 457 Query: 474 CTGAIVGYHPFGGFKMSG 491 C + FGG+K SG Sbjct: 458 CYHMYPAHAAFGGYKKSG 475 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: 568 Number of extensions: 30 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: 506 Length adjustment: 35 Effective length of query: 480 Effective length of database: 471 Effective search space: 226080 Effective search space used: 226080 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