Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate PP_2694 PP_2694 Aldehyde dehydrogenase family protein
Query= SwissProt::P94391 (515 letters) >FitnessBrowser__Putida:PP_2694 Length = 480 Score = 261 bits (666), Expect = 5e-74 Identities = 161/469 (34%), Positives = 240/469 (51%), Gaps = 14/469 (2%) Query: 35 KDYPLVINGERVETEAKIVSINPADKEEVVGRVSKASQEHAEQAIQAAAKAFEEWRYTSP 94 K Y I+G+ E A + + +P+D +++G+ +AS E A QAIQAA A W + Sbjct: 4 KTYNNYIDGQWCEGHATLGNYSPSDTGDLIGQYHQASAEQARQAIQAARAAQPLWAASGL 63 Query: 95 EERAAVLFRAAAKVRRRKHEFSALLVKEAGKPWNEADADTAEAIDFMEYYARQMIELAKG 154 E R VL ++ RK E LL +E GKP E + + F YYA +++ Sbjct: 64 ESRQQVLMAIGDELIARKEELGELLSREEGKPLAEGIGEVNRSGQFFHYYAAEVLRQMGE 123 Query: 155 KPVNSREGEKNQYVYTPTGVTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASATPVIA 214 + R G + P GV +I PWNF A A + GN VV KPA+ P A Sbjct: 124 TAASVRPGVDIEVHREPVGVVGIITPWNFPMATAAWKIAPALAFGNAVVFKPANLVPASA 183 Query: 215 AKFVEVLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSLITFTGSREVGTRIFERAAKVQ 274 E++ GLP G N V GSGA+VG+ L+ + +TFTGS + G R+ A Sbjct: 184 WALTEIISRQGLPSGTFNLVMGSGADVGEALIQSAEIDALTFTGSLQTGRRVAVATA--- 240 Query: 275 PGQQHLKRVIAEMGGKDTVVVDEDADIELAAQSIFTSAFGFAGQKCSAGSRAVVHEKVYD 334 +L R EMG K+ +VV +DAD+ELA + AF GQKC+A SR +V + ++D Sbjct: 241 ---GNLVRCQLEMGSKNALVVMDDADLELAVECALNGAFFGTGQKCTASSRLIVCDGIHD 297 Query: 335 QVLERV-IEITESKVTAKPDSADVYMGPVIDQGSYDKIMSYIEIGKQEG-RLVSGGTGDD 392 + +E + + + + KV A V +GPV D ++ ++Y+++ + EG L+ GG Sbjct: 298 RFVEALRLRMRQLKV-GHALEAGVQIGPVADARQLEQNLAYLQLAQAEGATLIEGGERLQ 356 Query: 393 --SKGYFIKPTIFADLDPKARLMQEEIFGPVVAFCKVSDFDEALEVANNTEYGLTGAVIT 450 GY+++P +F + R+ +EE+FGP+ +V DF+EAL N+TEYGLT +IT Sbjct: 357 LACDGYYMRPALFINSRNDMRINREEVFGPIACVIRVRDFEEALATLNDTEYGLTAGIIT 416 Query: 451 NNRKHIERAKQEFHVGNLYFNRNCTGAIVGYH-PFGGFKMSGTDSKAGG 498 + +H K+ G + N G YH PFGG K S + G Sbjct: 417 QSLRHASHFKRRAQTGCVMVNLPTAG--TDYHVPFGGRKASSFGPREQG 463 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: 530 Number of extensions: 25 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: 480 Length adjustment: 34 Effective length of query: 481 Effective length of database: 446 Effective search space: 214526 Effective search space used: 214526 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