Align delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial; EC 1.5.1.12 (characterized)
to candidate AO353_15035 AO353_15035 aldehyde dehydrogenase
Query= CharProtDB::CH_122352 (572 letters) >FitnessBrowser__pseudo3_N2E3:AO353_15035 Length = 496 Score = 155 bits (392), Expect = 4e-42 Identities = 144/475 (30%), Positives = 221/475 (46%), Gaps = 33/475 (6%) Query: 71 VIAGKE--VKSSSSLTQSNPASHGPVATYSNATAKDVQAAIESALEARKS--WASTPFAD 126 +I GK+ +S + NPA+ +A + DV AA+ SA +A +S W++ + Sbjct: 21 LIEGKQRPAQSGQTFAAINPATGAVLAEVAACGNADVDAAVISARQAFESGVWSARSPGE 80 Query: 127 RASVFLKAADLISTKYRYDVMALTMHGQGKNAWQAEIDSAAELCDFFRFGVKYAEDLYAQ 186 R V L+ A+LI R ++ L GK A FR+ + + LY Q Sbjct: 81 RKQVLLRLAELIMAN-REELALLDSLNMGKPVMDAYTIDVPGAAGVFRWYAESLDKLYDQ 139 Query: 187 QPVHHAPGVWNRVEY--RPLEGFVYAISPFNFTAIGGNLAGAPALM-GNVVVWKPSPSAI 243 AP N + R G V A+ P+NF APAL GN V+ KP+ + Sbjct: 140 I----APSAQNVLATITREALGVVAAVVPWNFPLDMAAWKLAPALAAGNSVILKPAEQSP 195 Query: 244 ASNWLVHQILLEAGLPKNVIQFVPGEAEEVTKTVLDHPDFAALHFTGSTNVFRNLYGQIS 303 S + ++ LEAG+P V+ +PG E+ K + H D L FTGST V + + Q S Sbjct: 196 FSALRLGELALEAGVPPGVLNVLPGLGEQAGKALGLHLDIDCLVFTGSTEVGK-YFMQYS 254 Query: 304 TRVAAGKYRSYPRIVGETGGKNFHLIHKSA-DIRNAAVQTVRGAFEYQGQKCSATSRVYV 362 + + ++ E GGK+ +L+ D+ AA + G F QG+ CSA SR+ V Sbjct: 255 AQ------SNLKQVWLECGGKSANLVFADCQDLDLAAQKAAFGIFFNQGEVCSANSRLLV 308 Query: 363 ASSIADSFLEQVASEAKSLKVGPPSDFTNFCGPVIHEASFTKLAKVIDEAKNDPELELLA 422 SI D F+E++ + + + G P D ++ G ++ ++ K I +A+ + Sbjct: 309 ERSIHDEFVERLMVQVERWQPGDPLDSSSTAGAIVDSRQTARIMKFIQQAERQGAKRVCG 368 Query: 423 G-GSYDSSKGWYIQPTVYRTTNPDHPLLTRELFGPILVVYAYPDATEADFARIAQKIDAT 481 G S + +IQPT++ D PL E+FGP+L V A+ D EA ++A Sbjct: 369 GQQSIINGSDNFIQPTIFTGVTADMPLFRDEVFGPVLAVTAFDD--EASALQLAN----D 422 Query: 482 GEYGLTGSVFAQDREALAVANDVLRN-AAGNFYINCKSTGAVVGQQPFGGARASG 535 YGL S++ D L A+ V R AG +N S A+ PFGG + SG Sbjct: 423 SVYGLAASLWTDD---LNRAHRVARQLRAGTVSVN--SVDALDVTVPFGGGKQSG 472 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: 566 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: 572 Length of database: 496 Length adjustment: 35 Effective length of query: 537 Effective length of database: 461 Effective search space: 247557 Effective search space used: 247557 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