Align Pyrroline-5-carboxylate reductase 2; P5C reductase 2; P5CR 2; PCA reductase 2; EC 1.5.1.2 (characterized)
to candidate WP_010531255.1 ON01_RS11815 pyrroline-5-carboxylate reductase
Query= SwissProt::P54552 (278 letters) >NCBI__GCF_000224785.1:WP_010531255.1 Length = 271 Score = 223 bits (569), Expect = 3e-63 Identities = 119/265 (44%), Positives = 171/265 (64%), Gaps = 1/265 (0%) Query: 2 KKIGFVGAGSMAEAMINGILQSGITKPEHIYITNRSNDERLIELKETYSVRPCRDKNEFF 61 +K+ F+GAGSMAE+++ GIL S E I++TN+S+ RL L++ Y V+ + + Sbjct: 3 EKLAFIGAGSMAESILTGILNSEFFPKEKIFVTNKSDKNRLEFLEKQYEVQNTDNTQQTV 62 Query: 62 THTDIIILAFKPKDAAESIDSIRPYI-KDQLVISVLAGLTIETIQHYFGRKLAVIRVMPN 120 DI+I+A KP D ++ SIR Y+ K QL+ISV+AG++ +TI +++ V+R MPN Sbjct: 63 DGADIVIIAVKPYDVEAALTSIRNYLDKGQLLISVVAGISTDTISQLINKEVPVVRAMPN 122 Query: 121 TSAAIRKSATGFSVSTEASKNDIIAAKALLETIGDATLVEERHLDAVTAIAGSGPAYVYR 180 TS+A +SAT + A + A L TIG AT V E + VTAI+GSGPAY+Y Sbjct: 123 TSSAAGQSATAVTRGKFAMAEHLQTALDLFNTIGTATEVAETDMHTVTAISGSGPAYIYY 182 Query: 181 YIEAMEKAAQKVGLDKETAKALILQTMAGATDMLLQSGKQPEKLRKEITSPGGTTEAGLR 240 +EAME AA + GLD +TA LI QT+ GA +ML SG P +LR+ ITSPGGTT+AGL Sbjct: 183 LVEAMELAAVRAGLDHDTAHDLITQTIVGAGEMLTTSGLDPSRLRENITSPGGTTQAGLE 242 Query: 241 ALQDSRFEEAIIHCIEETAKRSAEI 265 +L + F+E ++ C+E +RS E+ Sbjct: 243 SLAEHNFQETVMSCVESARERSIEL 267 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: 200 Number of extensions: 8 Number of successful extensions: 2 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: 271 Length adjustment: 25 Effective length of query: 253 Effective length of database: 246 Effective search space: 62238 Effective search space used: 62238 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_010531255.1 ON01_RS11815 (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.2124758.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-89 286.2 3.0 1.5e-89 286.1 3.0 1.0 1 NCBI__GCF_000224785.1:WP_010531255.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000224785.1:WP_010531255.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 286.1 3.0 1.5e-89 1.5e-89 1 263 [] 5 267 .. 5 267 .. 0.98 Alignments for each domain: == domain 1 score: 286.1 bits; conditional E-value: 1.5e-89 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilviers.eeklaalakelgvevtsdaeeavkeadvvllavKPqdl 72 +a+iGaG+m+e++l+g+l+++ k++i v+++s +++l+ l k+++v+ t + ++ v+ ad+v++avKP+d+ NCBI__GCF_000224785.1:WP_010531255.1 5 LAFIGAGSMAESILTGILNSEFFPKEKIFVTNKSdKNRLEFLEKQYEVQNTDNTQQTVDGADIVIIAVKPYDV 77 69********************************88889999999**************************** PP TIGR00112 73 eevlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevseeqkelve 145 e++l+++++ k++lliS++AG+++++++ql+++e +vvR+mPNt+++ g+++ta++ ++++ +e+ +++ NCBI__GCF_000224785.1:WP_010531255.1 78 EAALTSIRN-YLDKGQLLISVVAGISTDTISQLINKEVPVVRAMPNTSSAAGQSATAVTRGKFAMAEHLQTAL 149 ******999.5559*********************************************************** PP TIGR00112 146 ellkavGkvveveeklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaaklleesgeh 218 +l++++G+++ev+e ++++vta+sGSgPA++++l+ea++ a+v++GL++++a +l++qt+ Ga+++l+ sg + NCBI__GCF_000224785.1:WP_010531255.1 150 DLFNTIGTATEVAETDMHTVTAISGSGPAYIYYLVEAMELAAVRAGLDHDTAHDLITQTIVGAGEMLTTSGLD 222 ************************************************************************* PP TIGR00112 219 palLkdkVtsPgGtTiaglavLeekgvrsavieaveaavkrseeL 263 p++L++++tsPgGtT+agl++L e++++++v+ +ve+a +rs eL NCBI__GCF_000224785.1:WP_010531255.1 223 PSRLRENITSPGGTTQAGLESLAEHNFQETVMSCVESARERSIEL 267 *****************************************9887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (271 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: 17.98 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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