Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate WP_011612157.1 TERY_RS12430 aldehyde dehydrogenase family protein
Query= SwissProt::P94391 (515 letters) >NCBI__GCF_000014265.1:WP_011612157.1 Length = 490 Score = 264 bits (674), Expect = 6e-75 Identities = 170/481 (35%), Positives = 253/481 (52%), Gaps = 18/481 (3%) Query: 39 LVINGERVETEA--KIVSINPADKEEVVGRVSKASQEHAEQAIQAAAKAFE--EWRYTSP 94 L+IN E VE+ + + +INPA E V+ V++A ++A+ AA KAF EW S Sbjct: 18 LLINNEWVESASGKRFETINPATGE-VICNVAEADAPDVDKAVIAARKAFTSGEWPKISA 76 Query: 95 EERAAVLFRAAAKVRRRKHEFSALLVKEAGKPWNEA-DADTAEAIDFMEYYARQMIELAK 153 +R +L++ A + + E + L + GKP+ ++ + D AI YYA + + Sbjct: 77 AKRGELLYKLADLIEKNIEELARLETLDNGKPFKDSLNTDLPLAIACYRYYAG-WADKVQ 135 Query: 154 GKPVNSREGEKNQYVYTPTGVTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASATPVI 213 GK + + P GV I PWNF + A + GNT+V+K A TP+ Sbjct: 136 GKTIPISGPYFCYTRHEPVGVVGQIIPWNFPLLMQAWKLAPALAMGNTLVMKTAEQTPLS 195 Query: 214 AAKFVEVLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSLITFTGSREVGTRIFERAAKV 273 A + E++ E+G P GVVN + G G G + H + FTGS EVG I E AAK Sbjct: 196 ALRVGELVIEAGFPPGVVNILSGYGPTAGAAISHHKDIDKVAFTGSTEVGRLIMEAAAK- 254 Query: 274 QPGQQHLKRVIAEMGGKDTVVVDEDADIELAAQSIFTSAFGFAGQKCSAGSRAVVHEKVY 333 +LKRV E+GGK +V DAD++ A + + F GQ C AGSR V EK Y Sbjct: 255 ----SNLKRVTLELGGKSPNIVFADADMDAAIEGSHFALFFNQGQCCCAGSRLFVEEKCY 310 Query: 334 DQVLERVIEITESKVTAKPDSADVYMGPVIDQGSYDKIMSYIEIGKQEG-RLVSGGTGDD 392 D+ + + +E + ++ P + V GP +D+ ++K+MSYIE G+Q+G +++ GG+ Sbjct: 311 DEFVNKSVERAKLRMVGDPFTERVEQGPQVDEEQFNKVMSYIESGQQDGAQMLCGGSRVG 370 Query: 393 SKGYFIKPTIFADLDPKARLMQEEIFGPVVAFCKVSDFDEALEVANNTEYGLTGAVITNN 452 +GYFI PT+FAD+ ++ QEEIFGPV++ K D DE +E ANN+ YGL V T + Sbjct: 371 DRGYFIAPTVFADVQDNMKIAQEEIFGPVMSIIKFKDIDELVERANNSMYGLAAGVWTQD 430 Query: 453 RKHIERAKQEFHVGNLYFNRNCTGAIVGYHPFGGFKMSGTDSKAGGPDY-LALHMQAKTI 511 G ++ NC PFGGFK SG + G +Y L + + KT+ Sbjct: 431 VTKAHTLAHRLRAGTVWV--NCYDVFDAAAPFGGFKQSGLGRELG--EYGLQQYTEIKTV 486 Query: 512 S 512 + Sbjct: 487 T 487 Lambda K H 0.316 0.133 0.379 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: 611 Number of extensions: 30 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: 490 Length adjustment: 34 Effective length of query: 481 Effective length of database: 456 Effective search space: 219336 Effective search space used: 219336 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 (21.6 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