Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized)
to candidate WP_034273599.1 AMYHA_RS20335 aldehyde dehydrogenase family protein
Query= curated2:Q9K5Z5 (515 letters) >NCBI__GCF_000504245.1:WP_034273599.1 Length = 496 Score = 254 bits (649), Expect = 5e-72 Identities = 160/490 (32%), Positives = 251/490 (51%), Gaps = 34/490 (6%) Query: 39 LVINGERVTTDDKI---VSVNPAMKEQVIGVVSKASREIVDDAFKSAETAFHT--WKNVN 93 L I+G V T V +NPA + + V +A + VD A +A AF W+ Sbjct: 4 LFIDGRWVDTTGTAPARVVLNPANAAE-LATVCEADEKDVDAAVAAARRAFDDSPWRATT 62 Query: 94 PEERANILIRAAAIIRRRKHEFSAWLVKEAGKPWKEADADTAEAIDFLEYYARQMITLKD 153 ER +L A +++R K + + GK E D + YYA + + Sbjct: 63 ARERGELLREIARLLQRDKEHLARTESLDTGKTMAEGRVDVDDVTSVFRYYAN-LADNEA 121 Query: 154 GKPVNSREGEH-NRYFYTPIGVCVTISPWNFALAIMAGTTVAPIVTGNTVLLKPASTTPV 212 G+ V++ + +R + P+GVC I+PWN+ L M+ + GNTV++KP+ TP+ Sbjct: 122 GRVVDTGDASVISRVVHEPVGVCSLIAPWNYPLLQMSWKLAPALAAGNTVVMKPSEVTPL 181 Query: 213 VAAKFVEVLEEAGLPKGVVNFVPGSGTDIGDYLIDHPKTSLITFTGSRDVGVRLYERAAV 272 + + ++EEAG+P GVVN V G G ++G ++ HP L++FTG + G ++ AA Sbjct: 182 TTIELMRLVEEAGVPAGVVNLVLGGGANVGAPMVSHPDVDLVSFTGGLETGKKIMAMAA- 240 Query: 273 VHPGQQHLKRVIVEMGGKDTVVVDKDADLDLAAQSIVTSAFGFSGQKCSAGSRAVIHQDV 332 + +KRV +E+GGK+ VV DAD D A + +AF SGQ CSAGSR ++ D+ Sbjct: 241 -----EGVKRVALELGGKNPNVVFADADFDTAVDYALMAAFAHSGQVCSAGSRLIVESDI 295 Query: 333 YDVVLEKAVALTKQLSVGEPTAPDVYMGPVVDQGAFSKIMSYIEVGKEEG-RLMVGG--- 388 +D + + + +G+ P GP+ K+ +IE K EG RL+VGG Sbjct: 296 HDEFVAELARRADAIRLGDGLDPATECGPLSSAEHRDKVERHIEEAKTEGARLVVGGHRP 355 Query: 389 -EGDDSKGFFIQPTIFADVDPHARIMQEEIFGPVVAFSKARDFDHALEIANNTEYGLTGA 447 E + + G+F++PT+FAD D RI+Q+E+FGPVV + D A+ +AN+TEYGL GA Sbjct: 356 TEPELADGYFLRPTVFADCDREMRIVQDEVFGPVVTVERFDTEDEAIRLANDTEYGLAGA 415 Query: 448 VITTNRHHIEKAKRDFHVGNLYFNRNCTGAIVGYHPF------GGFKMSGTDSKAGGPDY 501 V T++ ++ G ++ N +HP+ GGF SG + GP Sbjct: 416 VWTSDASRAQRVAGALRHGTVWIN--------DFHPYLPQAEWGGFGKSGIGREL-GPSG 466 Query: 502 LALHMQAKTV 511 L + + K + Sbjct: 467 LEEYRETKHI 476 Lambda K H 0.318 0.135 0.394 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: 629 Number of extensions: 29 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: 496 Length adjustment: 34 Effective length of query: 481 Effective length of database: 462 Effective search space: 222222 Effective search space used: 222222 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 (21.7 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