Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; EC 1.5.1.2; PCA reductase (uncharacterized)
to candidate 353283 BT3757 pyrroline-5-carboxylate reductase (NCBI ptt file)
Query= curated2:P74572 (267 letters) >FitnessBrowser__Btheta:353283 Length = 257 Score = 128 bits (322), Expect = 1e-34 Identities = 84/258 (32%), Positives = 139/258 (53%), Gaps = 5/258 (1%) Query: 3 IQLGIIGGGVMAEAILARLIAEKTYAPEEIIVGEPHGARRDYLQKTYQ-VRVSPDNQEAA 61 +++ IIG G M +I L A +IIV P + + L++ + + + N EAA Sbjct: 1 MKIAIIGAGNMGGSIARGLAKGSLIADSDIIVSNPSAGKLEKLKEEFPGISTTLSNTEAA 60 Query: 62 NVSEVLLLAVKPQVLDRVLASLAGGANRPLVISILAGVSLQRIQKGF--PDHAIIRAMPN 119 ++V++LAVKP ++ V+ L + + LV S+ AG+S + + P+ + R +PN Sbjct: 61 TGADVVILAVKPWFVESVMRELKLKSKQTLV-SVAAGISFEELAHFVIAPEMPMFRLIPN 119 Query: 120 TPATVGAGMTAIAANKMVEPDQLAKAKAIFSAVGNVVEVPENLMDAVTGVSGSGPAYVAL 179 T + MT IAA + L + +F+ +G + +PE+ + A T ++ G AYV Sbjct: 120 TAISELESMTLIAARNTNDEQNLFMLR-LFNEMGMAMLIPEDKIAATTALTSCGIAYVLK 178 Query: 180 MIEALADGGVLAGLPRAIAQKLALQTVLGTAELIKETEEHPAQIKDKVTSPGGTTIAGVA 239 I+A G+ G+ A ++ Q+V G A LI + HP+ DKVT+PGG TI G+ Sbjct: 179 YIQAAMQAGIEMGIRPKDAMEMVAQSVKGAAALILNNDTHPSVEIDKVTTPGGITIKGIN 238 Query: 240 VLEKMGFRSAIIEAVRAA 257 LE GF SA+I+A++A+ Sbjct: 239 ELEHNGFTSAVIKAMKAS 256 Lambda K H 0.316 0.133 0.358 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: 143 Number of extensions: 10 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: 267 Length of database: 257 Length adjustment: 25 Effective length of query: 242 Effective length of database: 232 Effective search space: 56144 Effective search space used: 56144 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)
Align candidate 353283 BT3757 (pyrroline-5-carboxylate reductase (NCBI ptt file))
to HMM TIGR00112 (proC: pyrroline-5-carboxylate reductase (EC 1.5.1.2))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR00112.hmm # target sequence database: /tmp/gapView.11049.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00112 [M=263] Accession: TIGR00112 Description: proC: pyrroline-5-carboxylate reductase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-66 209.4 7.6 4.2e-66 209.3 7.6 1.0 1 lcl|FitnessBrowser__Btheta:353283 BT3757 pyrroline-5-carboxylate r Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Btheta:353283 BT3757 pyrroline-5-carboxylate reductase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 209.3 7.6 4.2e-66 4.2e-66 1 256 [. 3 256 .. 3 257 .] 0.95 Alignments for each domain: == domain 1 score: 209.3 bits; conditional E-value: 4.2e-66 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelg.vevtsdaeeavkeadvvllavKPqdleev 75 iaiiGaGnmg ++++gl k + +a+++i+v ++s+ kl++l +e+ +++t +++ea++ advv+lavKP +e+v lcl|FitnessBrowser__Btheta:353283 3 IAIIGAGNMGGSIARGLAKGSLIADSDIIVSNPSAGKLEKLKEEFPgISTTLSNTEAATGADVVILAVKPWFVESV 78 89***************************************99995599999************************ PP TIGR00112 76 laelkseektkeklliSilAGvtiekleqll.eaekrvvRvmPNtaakvgagvtaiaassevseeqkelveellka 150 ++elk + +++l+S++AG+++e+l + + + e ++ R++PNta + +++t iaa++ +++eq+ + +l+++ lcl|FitnessBrowser__Btheta:353283 79 MRELKL---KSKQTLVSVAAGISFEELAHFViAPEMPMFRLIPNTAISELESMTLIAARN-TNDEQNLFMLRLFNE 150 ***998...4569***************976145699*********************95.66778899******* PP TIGR00112 151 vGkvveveeklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaaklleesgehpalLkdkV 226 +G ++ ++e+++ a tal+ +g A+v+ i a+++ag+++G+ + a+e++aq +kGaa+l+ +++ hp++ +dkV lcl|FitnessBrowser__Btheta:353283 151 MGMAMLIPEDKIAATTALTSCGIAYVLKYIQAAMQAGIEMGIRPKDAMEMVAQSVKGAAALILNNDTHPSVEIDKV 226 **************************************************************************** PP TIGR00112 227 tsPgGtTiaglavLeekgvrsavieaveaa 256 t+PgG Ti+g+++Le++g+ savi+a++a+ lcl|FitnessBrowser__Btheta:353283 227 TTPGGITIKGINELEHNGFTSAVIKAMKAS 256 ***************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (257 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 7.69 // [ok]
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