Align pyrroline-5-carboxylate reductase (EC 1.5.1.2) (characterized)
to candidate WP_027178039.1 G496_RS0103405 pyrroline-5-carboxylate reductase
Query= reanno::DvH:207819 (265 letters) >NCBI__GCF_000429985.1:WP_027178039.1 Length = 267 Score = 229 bits (584), Expect = 5e-65 Identities = 121/264 (45%), Positives = 168/264 (63%), Gaps = 1/264 (0%) Query: 1 MQTTLGCIGCGNMGSAILRGLSGREGLRLVGCDPTGAKLAAL-ADAGVEGVADIAAAVRA 59 M +G IG GNMG+AI++G++G + + L+G D L L + G++ + Sbjct: 1 MSIKVGFIGTGNMGTAIIKGMAGNKDIELLGFDLNSEILEKLNKECGLKAKSSARELATE 60 Query: 60 SDIVLVAVKPGQVGAVLGAAMPELDSGKVVVSIASGVSVGSLREMSGGRCPVVRVMPNTP 119 SD V++AVKP VL EL+ K ++SIA+G++V L+E +G CPVVRVMPNTP Sbjct: 61 SDFVVLAVKPQYAENVLEDITQELNDKKCLISIAAGLTVDRLKEFTGNSCPVVRVMPNTP 120 Query: 120 AMVGAGVFALCFEDATLDEVRRTLVKELFEALGRVLVLPEEKFNAFTAVVGCGPAYVFHF 179 A+V GVFA+C +D L + ++ +FE+LG V +L E++F+AFT V+G GPAY+F+F Sbjct: 121 ALVNEGVFAVCIDDKHLTDAQKEFAGVMFESLGDVHILSEKQFDAFTGVIGSGPAYIFYF 180 Query: 180 MEAVVEAAVTLGFPRHEATDMVVDLFAGSVKLAATSGTHLSLLREAVCSPAGNTIAAMNQ 239 MEA++E+ V LG R +AT MV LFAGS KLA S H+S LRE V SPAG T+ A+ Sbjct: 181 MEALIESGVELGLTRPQATSMVSKLFAGSTKLAIESDKHISELREMVTSPAGTTVEALVH 240 Query: 240 FDRDAVRGRIIDAILAAYRRGQEM 263 DR A R IIDA+ Y R E+ Sbjct: 241 LDRTATRANIIDAVHKCYERSIEL 264 Lambda K H 0.322 0.137 0.393 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: 166 Number of extensions: 3 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: 265 Length of database: 267 Length adjustment: 25 Effective length of query: 240 Effective length of database: 242 Effective search space: 58080 Effective search space used: 58080 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 47 (22.7 bits)
Align candidate WP_027178039.1 G496_RS0103405 (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.12716.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.6e-83 265.2 0.1 4e-83 265.0 0.1 1.0 1 lcl|NCBI__GCF_000429985.1:WP_027178039.1 G496_RS0103405 pyrroline-5-carbo Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000429985.1:WP_027178039.1 G496_RS0103405 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 265.0 0.1 4e-83 4e-83 1 263 [] 5 264 .. 5 264 .. 0.96 Alignments for each domain: == domain 1 score: 265.0 bits; conditional E-value: 4e-83 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKP 69 +++iG Gnmg+a+++g+ ++ e+l + ++e l++l ke g +++s+a+e+++e+d+v+lavKP lcl|NCBI__GCF_000429985.1:WP_027178039.1 5 VGFIGTGNMGTAIIKGMAGNKD---IELLGFDLNSEILEKLNKECGLKAKSSARELATESDFVVLAVKP 70 68**************988744...589999999*********************************** PP TIGR00112 70 qdleevlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevse 138 q +e+vl+++++ e + +k+liSi+AG+t+++l++ ++++++vvRvmPNt+a v++gv a++ +++ lcl|NCBI__GCF_000429985.1:WP_027178039.1 71 QYAENVLEDITQ-ELNDKKCLISIAAGLTVDRLKEFTGNSCPVVRVMPNTPALVNEGVFAVCIDDKHLT 138 *********999.66689******************************************998766655 PP TIGR00112 139 e.qkelveellkavGkvveveeklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlk 206 + qke + +++++G+v+ ++ek++da+t++ GSgPA++f+++eal+++gv+lGL+r +a+++++++++ lcl|NCBI__GCF_000429985.1:WP_027178039.1 139 DaQKEFAGVMFESLGDVHILSEKQFDAFTGVIGSGPAYIFYFMEALIESGVELGLTRPQATSMVSKLFA 207 55******************************************************************* PP TIGR00112 207 GaaklleesgehpalLkdkVtsPgGtTiaglavLeekgvrsavieaveaavkrseeL 263 G+ kl es++h ++L++ VtsP+GtT+++l L + + r+ +i+av+++++rs eL lcl|NCBI__GCF_000429985.1:WP_027178039.1 208 GSTKLAIESDKHISELREMVTSPAGTTVEALVHLDRTATRANIIDAVHKCYERSIEL 264 *****************************************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (267 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: 9.11 // [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