Align delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial; EC 1.5.1.12 (characterized)
to candidate AO356_09270 AO356_09270 aldehyde dehydrogenase
Query= CharProtDB::CH_122352 (572 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_09270 Length = 505 Score = 158 bits (400), Expect = 4e-43 Identities = 144/491 (29%), Positives = 223/491 (45%), Gaps = 35/491 (7%) Query: 73 AGKEVKSSSSLTQSNPASHGPVATYSNATAKDVQAAIESALEARKS--WASTPFADRASV 130 A K S ++ NPA+ + S A+DV A+ A EA + W P +R +V Sbjct: 28 AFKPAISGNTFATVNPATGELLTEVSACAAEDVDYAVSKAREAFEDGRWRLLPPGERKAV 87 Query: 131 FLKAADLISTKYRYDVMALTMHGQGKNAWQAEIDSAAELCDFFRFGVKYAEDLYAQQPVH 190 LK A L+ K R+++ L GK + ++ + R+ + + LY H Sbjct: 88 LLKFAKLLE-KNRHELAVLESLDSGKPVRECQLVDVPDTIHTLRWHAEVIDKLYD----H 142 Query: 191 HAP---GVWNRVEYRPLEGFVYAISPFNFTAIGGNLAGAPALM-GNVVVWKPSPSAIASN 246 AP V P+ G V + P+NF + PAL G V+ KP+ + Sbjct: 143 TAPVGNDALTMVVREPI-GVVGCVLPWNFPLLMLAWKIGPALAAGCSVIVKPAEQTTLTT 201 Query: 247 WLVHQILLEAGLPKNVIQFVPGEAEEVTKTVLDHPDFAALHFTGSTNVFRNLYGQISTRV 306 V ++ +AG+P V+ V G ++V + + H D + FTGST R + Sbjct: 202 LRVAELAFDAGVPAGVLNIVTGTGKDVGEPLGLHKDVDMVSFTGSTATGRRFLHYAADS- 260 Query: 307 AAGKYRSYPRIVGETGGKNFHLIHKSA-DIRNAAVQTVRGAFEYQGQKCSATSRVYVASS 365 + R+V E GGKN ++ A D+ A Q V GAF G+ CSATSR+ V +S Sbjct: 261 ------NLKRVVLECGGKNPAVVMDDAEDLDLVAEQVVNGAFWNMGENCSATSRLLVHAS 314 Query: 366 IADSFLEQVASEAKSLKVGPPSDFTNFCGPVIHEASFTKLAKVIDEAKNDPELELLAGGS 425 + D L+++ + + K+G P D N G ++ F K+ +D A + LE + GG Sbjct: 315 VKDELLKRMGAYIREWKMGDPLDPQNRVGALVSSDHFEKVKSYLDYA-SASNLEAVYGG- 372 Query: 426 YDSSKGWYIQPTVYRTTNPDHPLLTRELFGPILVVYAYPDATEADFARIAQKIDATGEYG 485 D+ G +IQPTV + D L E+FGP+L V + EA IA D YG Sbjct: 373 -DTHDGAFIQPTVIDGVDRDSRLFQEEIFGPVLSVTTFNSICEA----IALANDT--HYG 425 Query: 486 LTGSVFAQD-REALAVANDVLRNAAGNFYINCKSTGAVVGQQPFGGARASGTNDKAGSGN 544 L SV+ + R A+ +A ++ AG +NC G PFGG + SG + S Sbjct: 426 LAASVYTGNLRRAIKLAREI---RAGIVTVNCFGEGD--ASTPFGGYKESGFGGRDKSVF 480 Query: 545 LLSRFVSLRSI 555 ++ +++I Sbjct: 481 AHDQYTEIKTI 491 Lambda K H 0.316 0.130 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: 641 Number of extensions: 34 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: 572 Length of database: 505 Length adjustment: 35 Effective length of query: 537 Effective length of database: 470 Effective search space: 252390 Effective search space used: 252390 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