Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; EC 1.5.1.2; PCA reductase (uncharacterized)
to candidate WP_036260002.1 DL86_RS07785 pyrroline-5-carboxylate reductase
Query= curated2:P74572 (267 letters) >NCBI__GCF_000746085.1:WP_036260002.1 Length = 274 Score = 162 bits (410), Expect = 7e-45 Identities = 104/211 (49%), Positives = 134/211 (63%), Gaps = 8/211 (3%) Query: 60 AANVSEVLLLAVKPQVLDR--VLASLAGGANRPLVISILAGVSLQRIQKGFPD-HAIIRA 116 AAN EVL+LA+KPQVLD VLA LAG R LVIS+LAG ++ I FP HAI+RA Sbjct: 64 AANPPEVLVLAIKPQVLDEAGVLAPLAGP--RTLVISVLAGKTIANISARFPQAHAIVRA 121 Query: 117 MPNTPATVGAGMTAIAANKMVEPDQLAKAKAIFSAVGNVVEVP-ENLMDAVTGVSGSGPA 175 MPN PA VG G+ +AAN+ V +Q A A+A+ A G + + E L+DAVT VSGSGPA Sbjct: 122 MPNLPAAVGRGIAGVAANETVTLEQRALAEALLGATGRIEWLADEGLIDAVTAVSGSGPA 181 Query: 176 YVALMIEALADGGVLAGLPRAIAQKLALQTVLGTAELI-KETEEHPAQIKDKVTSPGGTT 234 YV + E LA G GLP A +LA TV G EL+ + PA++++ VTS GGTT Sbjct: 182 YVFYLAECLAQAGAALGLPADAAARLARATVEGAGELLFRNDASTPAELRESVTSRGGTT 241 Query: 235 IAGVAVLEKMGFRSAIIE-AVRAAYRRSQEL 264 A + VL + +IE AV+AA +R++ L Sbjct: 242 AAALEVLMAQDGLAPLIERAVKAAQQRAEAL 272 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: 217 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: 274 Length adjustment: 25 Effective length of query: 242 Effective length of database: 249 Effective search space: 60258 Effective search space used: 60258 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 WP_036260002.1 DL86_RS07785 (pyrroline-5-carboxylate reductase)
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.aa/TIGR00112.hmm # target sequence database: /tmp/gapView.2389.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.7e-70 221.9 4.2 6.5e-70 221.7 4.2 1.0 1 lcl|NCBI__GCF_000746085.1:WP_036260002.1 DL86_RS07785 pyrroline-5-carboxy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000746085.1:WP_036260002.1 DL86_RS07785 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 221.7 4.2 6.5e-70 6.5e-70 2 263 .] 14 272 .. 13 272 .. 0.91 Alignments for each domain: == domain 1 score: 221.7 bits; conditional E-value: 6.5e-70 TIGR00112 2 aiiGaGnmgeallsgllkkgakakkeilviers.eeklaalakelgvevtsdaeeavkeadvvllavKP 69 ++ GaG+mg a+l ++l +g + +i vi+++ + + +la++ g + ++ a++ +v++la+KP lcl|NCBI__GCF_000746085.1:WP_036260002.1 14 VLAGAGKMGGAMLLAWLDQGLD-PRRIGVIDPQpSRTILELAAARGFTLNA----AANPPEVLVLAIKP 77 678***************9775.9*******99555666666666665555....467889******** PP TIGR00112 70 qdleevlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevse 138 q+l+e+ l+ + +l+iS+lAG ti++++ +++ +++vR+mPN++a+vg+g++++aa+++v+ lcl|NCBI__GCF_000746085.1:WP_036260002.1 78 QVLDEAGV-LAP-LAGPRTLVISVLAGKTIANISARFPQAHAIVRAMPNLPAAVGRGIAGVAANETVTL 144 ***98654.444.344899************************************************** PP TIGR00112 139 eqkelveellkavGkvveve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlk 206 eq++l+e+ll a+G + +++ e l+davta+sGSgPA+vf+l+e+la+ag +lGLp++ a +la++t++ lcl|NCBI__GCF_000746085.1:WP_036260002.1 145 EQRALAEALLGATGRIEWLAdEGLIDAVTAVSGSGPAYVFYLAECLAQAGAALGLPADAAARLARATVE 213 ********************9************************************************ PP TIGR00112 207 Gaaklleesge.hpalLkdkVtsPgGtTiaglavLeekg.vrsavieaveaavkrseeL 263 Ga++ll +++ +pa+L++ Vts gGtT+a+l+vL++++ + +++av+aa +r+e L lcl|NCBI__GCF_000746085.1:WP_036260002.1 214 GAGELLFRNDAsTPAELRESVTSRGGTTAAALEVLMAQDgLAPLIERAVKAAQQRAEAL 272 ******888667**********************9987659**************9976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (274 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 7.23 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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