Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate Ga0059261_3374 Ga0059261_3374 NAD-dependent aldehyde dehydrogenases
Query= SwissProt::P94391 (515 letters) >FitnessBrowser__Korea:Ga0059261_3374 Length = 474 Score = 220 bits (560), Expect = 1e-61 Identities = 152/478 (31%), Positives = 242/478 (50%), Gaps = 24/478 (5%) Query: 41 INGERVETEA--KIVSINPADKEEVVGRVSKASQEHAEQAIQAAAKAFEEWRYTSPEERA 98 I GE VE+E + INPA E V ++ S+ A++A+ AA AF+ + TS +ER Sbjct: 9 IGGEWVESEGGTRHDVINPAT-EAPVTEITLGSEADADKAVAAAKAAFDSFSRTSVDERI 67 Query: 99 AVLFRAAAKVRRRKHEFSALLVKEAGKPWNEAD-ADTAEAIDFMEYYARQMIELAKGKPV 157 A+L A+ + R + + + E G P + A A I + I K Sbjct: 68 ALLEAILAEYKNRAGDLADAIAAEMGAPISLAKTAQVGSGIGHL----MSTINALKAFEF 123 Query: 158 NSREGEKNQYVYTPTGVTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASATPVIAAKF 217 + + G+ + V+ P GV +I PWN+ + + GNT+VLKP+ P AA F Sbjct: 124 SEQIGQ-SLVVHEPIGVVALITPWNWPLNQIVAKVAPALAAGNTMVLKPSEEAPGSAAIF 182 Query: 218 VEVLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSLITFTGSREVGTRIFERAAKVQPGQ 277 E+++++G+P GV N V G G VG L H +++FTGS G ++ + AA+ Sbjct: 183 AEIMDKAGVPAGVFNLVQGDGPIVGTALSRHRDVDMVSFTGSTRAGIQVAKNAAET---- 238 Query: 278 QHLKRVIAEMGGKDTVVVDEDADIELAAQSIFTSAFGFAGQKCSAGSRAVVHEKVYDQVL 337 +KRV E+GGK V+ AD+ A Q S +GQ C A +R +VHE + Sbjct: 239 --VKRVHQELGGKSPNVILPGADLSRAVQVGLFSVVMNSGQSCIAPARMLVHESQAAEAA 296 Query: 338 ERVIEITESKVTAKPDSADVYMGPVIDQGSYDKIMSYIEIGKQEG-RLVSGGTGDD---S 393 + + ++ T P ++GPV+++ ++KI I G +EG +L +GG G Sbjct: 297 QIASGLMKAVETGDPAQEGRHIGPVVNKAQWEKIQGLIRKGMEEGAKLETGGPGRPDGIE 356 Query: 394 KGYFIKPTIFADLDPKARLMQEEIFGPVVAFCKVSDFDEALEVANNTEYGLTGAVITNNR 453 GYF+KPT+F+ + + +EEIFGPV+ D +EA+ +AN+T+YGL+ AV+ + Sbjct: 357 TGYFVKPTLFSGVRNDMTIAREEIFGPVITIIPYRDEEEAVRIANDTDYGLS-AVLFGSP 415 Query: 454 KHIERAKQEFHVGNLYFNRNCTGAIVGYHPFGGFKMSGTDSKAGGPDYLALHMQAKTI 511 + ++R G +Y N + PFGG+K SG + + G LA M+ K + Sbjct: 416 EEVKRVAPRLRAGMVYINGGQPDPSL---PFGGYKQSG-NGREHGKFGLAEFMEVKAM 469 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: 607 Number of extensions: 33 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: 474 Length adjustment: 34 Effective length of query: 481 Effective length of database: 440 Effective search space: 211640 Effective search space used: 211640 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 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