Align 1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase (NADPH) (EC 1.5.1.21) (characterized)
to candidate HSERO_RS22840 HSERO_RS22840 ornithine cyclodeaminase
Query= BRENDA::O54983 (313 letters) >FitnessBrowser__HerbieS:HSERO_RS22840 Length = 306 Score = 132 bits (331), Expect = 1e-35 Identities = 97/310 (31%), Positives = 155/310 (50%), Gaps = 25/310 (8%) Query: 7 FLSAEEVQDHLRSSSLLIPPLEAALANFSKGPDGGVMQPVRTVVPVAKHRGFLGVMPAYS 66 FLS +++ + L + + EA F+ +G VRT A + L +M A Sbjct: 3 FLSNQQISELLTTEDAIAAMREA----FAGAAEGAHQGRVRTS---ASNGVMLSMMGAVI 55 Query: 67 AAEDALTTKLVTFYEGHSNTAVPSHQASVLLFDPSNGSLLAVMDGNVITAKRTAAVSAIA 126 A K+ T +G + LF G+ L M+G+ +T RTAA +A+A Sbjct: 56 PAAGIAGAKVYTTIKGQFRFVIQ-------LFSTETGAPLCTMEGDAMTGLRTAAATAVA 108 Query: 127 TKLLKPPGSDVLCILGAGVQAYSHYEIFTEQFSFKEVRMWNRTREN--AEKFASTVQGDV 184 L P + VL ++G GVQA SH + FKEV + R+ + AE+ T+ Sbjct: 109 CDALARPDAGVLAVIGTGVQARSHIPALLQVRPFKEVLIAGRSGQQALAEEVTRTLGVPA 168 Query: 185 RVCSSVQEAVTGADVIITVTMATEPILFGEWVKPGAHINAVGASRPDWRELDDELM-RQA 243 R+ S+ EA ADV++TVT + P+ GE ++PGA + AVGAS+ + RELDD + R A Sbjct: 169 RMV-SIDEAAAQADVLVTVTRSATPLFDGELLRPGAFVAAVGASKANVRELDDTAIGRAA 227 Query: 244 VLYVDSREAALKESGDVLLSGADIF-----AELGEVISGAKP--AHCEKTTVFKSLGMAV 296 L+V+ + A +E+GD++ +F EL + + G+ P + ++K +G+ + Sbjct: 228 ALFVEWKPQAQQEAGDLVQCAPGVFDWAQVMELAQAVDGSMPYQRRPDDIVIYKGIGIGL 287 Query: 297 EDLVAAKLVY 306 ED+ A L Y Sbjct: 288 EDVALAGLAY 297 Lambda K H 0.316 0.131 0.376 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: 224 Number of extensions: 16 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: 313 Length of database: 306 Length adjustment: 27 Effective length of query: 286 Effective length of database: 279 Effective search space: 79794 Effective search space used: 79794 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: 48 (23.1 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