Align Pyrroline-5-carboxylate reductase 2; P5C reductase 2; P5CR 2; PCA reductase 2; EC 1.5.1.2 (characterized)
to candidate PP_3778 PP_3778 Pyrroline-5-carboxylate reductase
Query= SwissProt::P54552 (278 letters) >FitnessBrowser__Putida:PP_3778 Length = 264 Score = 116 bits (291), Expect = 4e-31 Identities = 84/271 (30%), Positives = 143/271 (52%), Gaps = 15/271 (5%) Query: 1 MKKIGFVGAGSMAEAMINGILQ--SGITKPEHIYI-TNRSNDERLIELKETYSVRPCRDK 57 MK I VGAG M A++ G+ T I I T RSND R + + ++ + + Sbjct: 1 MKTIYMVGAGHMGGAILLGLKAYFKSATDLRVIEIDTQRSNDWRAKGFETSSRIQTLQPQ 60 Query: 58 NEFFTHTDIIILAFKPKDAAESIDSIRPYIKDQL--VISVLAGLTIETIQHYFGRKLAVI 115 D ++LA P+ E++ + P + V+SV+AG+T T+ G AV+ Sbjct: 61 -------DCVVLAVPPQQF-ENMLAANPVLCRHRGPVVSVMAGITHATLVRLLGHD-AVV 111 Query: 116 RVMPNTSAAIRKSATGFSVSTEASKNDIIAAKALLETIGDATLV-EERHLDAVTAIAGSG 174 R +PNT + + + T + ++A I +A+ + + IG + V +ER +D TA+AG G Sbjct: 112 RAIPNTPSEVAQGVTMYYAPSDADAALIDSARQIFDVIGLSLRVNDERQIDTGTALAGGG 171 Query: 175 PAYVYRYIEAMEKAAQKVGLDKETAKALILQTMAGATDMLLQSGKQPEKLRKEITSPGGT 234 PA V + +A++ +GLD E A + LQ ++G ++ SGK ++ +E+ + GGT Sbjct: 172 PALVAHFADALQDYGLHMGLDSEQAAVVALQLLSGTAALIQASGKPASQICQEVQTAGGT 231 Query: 235 TEAGLRALQDSRFEEAIIHCIEETAKRSAEI 265 TE +RAL + F+ + ++ A+RSAE+ Sbjct: 232 TERAIRALDAAGFKGLVNAALDAAARRSAEL 262 Lambda K H 0.316 0.131 0.353 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: 161 Number of extensions: 11 Number of successful extensions: 3 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: 278 Length of database: 264 Length adjustment: 25 Effective length of query: 253 Effective length of database: 239 Effective search space: 60467 Effective search space used: 60467 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: 47 (22.7 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