Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate Pf6N2E2_3298 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26)
Query= SwissProt::P94391 (515 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3298 Length = 481 Score = 267 bits (682), Expect = 7e-76 Identities = 164/472 (34%), Positives = 244/472 (51%), Gaps = 20/472 (4%) Query: 35 KDYPLVINGERVETEAKIVSINPADKEEVVGRVSKASQEHAEQAIQAAAKAFEEWRYTSP 94 K + ING+ V +INP+D +V+G +KA AI+AA AF W + Sbjct: 5 KRFDNYINGQWVAGADYCTNINPSDLSDVIGEYAKADAAQVNAAIEAARAAFPAWSTSGI 64 Query: 95 EERAAVLFRAAAKVRRRKHEFSALLVKEAGKPWNEADADTAEAIDFMEYYARQMIELAKG 154 + R L + +++ R+ E LL +E GK EA + A + +++A + + L+ Sbjct: 65 QARHDALDKVGSEILARREELGQLLAREEGKTLPEAIGEVTRAGNIFKFFAGECLRLSGD 124 Query: 155 KPVNSREGEKNQYVYTPTGVTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASATPVIA 214 + R G + GV +I PWNF AI A + GN VV+KPA P A Sbjct: 125 YVPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVIKPAELVPGCA 184 Query: 215 AKFVEVLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSLITFTGS----REVGTRIFERA 270 E++ +G P G N V GSG VGD LV+ PK I+FTGS R++ R Sbjct: 185 WALAEIISRAGFPAGAFNLVMGSGRVVGDILVNSPKVDGISFTGSVGVGRQIAVNCVSRQ 244 Query: 271 AKVQPGQQHLKRVIAEMGGKDTVVVDEDADIELAAQSIFTSAFGFAGQKCSAGSRAVVHE 330 AKVQ EMGGK+ ++ +DAD++ A + SAF GQ+C+A SR +V Sbjct: 245 AKVQ----------LEMGGKNPQIILDDADLKQAVELAVQSAFYSTGQRCTASSRLIVTA 294 Query: 331 KVYDQVLERVIEITESKVTAKPDSADVYMGPVIDQGSYDKIMSYIEIGKQEG-RLVSGG- 388 ++D+ + + E +S A +GPV+ + + + YI+IG+ EG RLVSGG Sbjct: 295 GIHDKFVAAMAERMQSIKVGHALKAGTDIGPVVSEAQLSQDLKYIDIGQSEGARLVSGGG 354 Query: 389 -TGDDSKGYFIKPTIFADLDPKARLMQEEIFGPVVAFCKVSDFDEALEVANNTEYGLTGA 447 D++GYF+ PT+FAD + R+ +EEIFGPV +V+D++ AL +AN+TE+GL+ Sbjct: 355 LVTCDTEGYFLAPTLFADSEASMRISREEIFGPVANVVRVADYEAALAMANDTEFGLSAG 414 Query: 448 VITNNRKHIERAKQEFHVGNLYFNRNCTGAIVGYH-PFGGFKMSGTDSKAGG 498 + T + K+ K+ G + N G V YH PFGG K S S+ G Sbjct: 415 IATTSLKYANHFKRHSQAGMVMVNLPTAG--VDYHVPFGGRKGSSYGSREQG 464 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: 575 Number of extensions: 23 Number of successful extensions: 3 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: 481 Length adjustment: 34 Effective length of query: 481 Effective length of database: 447 Effective search space: 215007 Effective search space used: 215007 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