Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate Ac3H11_612 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26)
Query= SwissProt::P94391 (515 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_612 Length = 483 Score = 257 bits (657), Expect = 6e-73 Identities = 161/475 (33%), Positives = 236/475 (49%), Gaps = 13/475 (2%) Query: 40 VINGERVETEAKIVSINPADKEEVVGRVSKASQEHAEQAIQAAAKAFEEWRYTSPEERAA 99 +ING +S NP+D EVV ++A + E A++AAA A W ++P+ RA Sbjct: 13 LINGRWEIGTTTGISTNPSDTREVVAEYARADRNQTELAVRAAADALPTWSQSTPQRRAD 72 Query: 100 VLFRAAAKVRRRKHEFSALLVKEAGKPWNEADADTAEAIDFMEYYARQMIELAKGKPVNS 159 VL +++ RK E ALL +E GK E A+ A + +++A + + + + Sbjct: 73 VLDMIGSELLARKDELGALLAREEGKTLPEGVAEVARSGQIFKFFAGEALRIQGELLASV 132 Query: 160 REGEKNQYVYTPTGVTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASATPVIAAKFVE 219 R+G + P GV +I PWNF FAI A + GNTVV KPA P E Sbjct: 133 RQGVQVDVTREPVGVVGIIAPWNFPFAIPAWKIAPALAYGNTVVFKPAELVPACGWALAE 192 Query: 220 VLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSLITFTGSREVGTRIFERAAKVQPGQQH 279 ++ SGLP G N + GSG EVG LVDHP + ++FTGS G RI A+ Q Sbjct: 193 IISRSGLPAGAFNLIMGSGREVGQTLVDHPLVNALSFTGSVATGDRILRAAS------QR 246 Query: 280 LKRVIAEMGGKDTVVVDEDADIELAAQSIFTSAFGFAGQKCSAGSRAVVHEKVYDQVLER 339 +V EMGGK+ ++V DAD++ A ++ GQ+C+A SR +V +V+D + R Sbjct: 247 RAKVQLEMGGKNPLIVLADADLDQAVDCALQGSYFSTGQRCTASSRLIVEAEVHDAFVAR 306 Query: 340 VIEITESKVTAKPDSADVYMGPVIDQGSYDKIMSYIEIGKQEG-RLVSGGTGDD--SKGY 396 + S MGPV+D + + YI+I K EG V GG + + G+ Sbjct: 307 LRNRLASLKVGHALERGTEMGPVVDDNQLAQNLGYIDIAKSEGAEHVWGGERLERPTPGH 366 Query: 397 FIKPTIFADLDPKARLMQEEIFGPVVAFCKVSDFDEALEVANNTEYGLTGAVITNNRKHI 456 ++ P +F P+ R+ +EEIFGPV + D+D AL +AN+T +GL + T + K Sbjct: 367 YMSPALFL-ARPEHRVAREEIFGPVACVLRADDYDHALALANDTPFGLCAGICTTSLKRA 425 Query: 457 ERAKQEFHVGNLYFNRNCTGAIVGYH-PFGGFKMSGTDSKAGGPDYLALHMQAKT 510 K+ VG N G V +H PFGG K S ++ G + KT Sbjct: 426 MHFKRHAAVGMTMVNLPTAG--VDFHVPFGGRKESSYGAREQGRYAAEFYTTVKT 478 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: 549 Number of extensions: 33 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: 483 Length adjustment: 34 Effective length of query: 481 Effective length of database: 449 Effective search space: 215969 Effective search space used: 215969 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