Align pyrroline-5-carboxylate reductase (EC 1.5.1.2) (characterized)
to candidate 207819 DVU2332 pyrroline-5-carboxylate reductase
Query= metacyc::MONOMER-7803 (277 letters) >MicrobesOnline__882:207819 Length = 265 Score = 157 bits (397), Expect = 2e-43 Identities = 97/266 (36%), Positives = 150/266 (56%), Gaps = 8/266 (3%) Query: 14 LGFVGAGNLAESIARGVAASGVLPASAVRTAPHRRPERAAAFASLGATILASNAQVVDDS 73 LG +G GN+ +I RG+ SG V P + AA A G +A A V S Sbjct: 5 LGCIGCGNMGSAILRGL--SGREGLRLVGCDP--TGAKLAALADAGVEGVADIAAAVRAS 60 Query: 74 DVIVISVKPQIVKQVLVELKPLLSEEKLLVSIAAGIKMKDLQDWSGQR-RIIRVMPNTPS 132 D+++++VKP V VL P L K++VSIA+G+ + L++ SG R ++RVMPNTP+ Sbjct: 61 DIVLVAVKPGQVGAVLGAAMPELDSGKVVVSIASGVSVGSLREMSGGRCPVVRVMPNTPA 120 Query: 133 AVGQAASVMCLGETATENDENR--VKSLFSAIGKVWTAEEKYFDAVTGLSGSGPAYIFLA 190 VG +C E AT ++ R VK LF A+G+V E+ F+A T + G GPAY+F Sbjct: 121 MVGAGVFALCF-EDATLDEVRRTLVKELFEALGRVLVLPEEKFNAFTAVVGCGPAYVFHF 179 Query: 191 IEAMADGGVAAGLPRDLALGLAAQTVLGAATMVSETGKHPGQLKDQVTSPAGTTIAGVHE 250 +EA+ + V G PR A + G+ + + +G H L++ V SPAG TIA +++ Sbjct: 180 MEAVVEAAVTLGFPRHEATDMVVDLFAGSVKLAATSGTHLSLLREAVCSPAGNTIAAMNQ 239 Query: 251 LEKGSFRGTLINAVVAATTRCRELSK 276 ++ + RG +I+A++AA R +E+ + Sbjct: 240 FDRDAVRGRIIDAILAAYRRGQEMER 265 Lambda K H 0.315 0.130 0.362 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: 187 Number of extensions: 17 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: 277 Length of database: 265 Length adjustment: 25 Effective length of query: 252 Effective length of database: 240 Effective search space: 60480 Effective search space used: 60480 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 207819 DVU2332 (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.carbon/TIGR00112.hmm # target sequence database: /tmp/gapView.10807.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-76 243.9 0.8 1.2e-76 243.8 0.8 1.0 1 lcl|MicrobesOnline__882:207819 DVU2332 pyrroline-5-carboxylate Domain annotation for each sequence (and alignments): >> lcl|MicrobesOnline__882:207819 DVU2332 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 243.8 0.8 1.2e-76 1.2e-76 2 263 .] 6 263 .. 5 263 .. 0.94 Alignments for each domain: == domain 1 score: 243.8 bits; conditional E-value: 1.2e-76 TIGR00112 2 aiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKPqdleevlaelk 80 + iG+Gnmg+a+l+gl+ ++ +++ +++ +klaala ++gve ++d ++av+++d+vl+avKP ++ +vl lcl|MicrobesOnline__882:207819 6 GCIGCGNMGSAILRGLSGREG---LRLVGCDPTGAKLAALA-DAGVEGVADIAAAVRASDIVLVAVKPGQVGAVLGAAM 80 78*************998744...45666776677777666.56788889999**********************9766 PP TIGR00112 81 seektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevsee.qkelveellkavGkvveve 158 e +k+++Si+ Gv++ l+++ +++++vvRvmPNt+a+vgagv a++ ++++ +e +++lv+el++a+G v+ ++ lcl|MicrobesOnline__882:207819 81 P-ELDSGKVVVSIASGVSVGSLREMSGGRCPVVRVMPNTPAMVGAGVFALCFEDATLDEvRRTLVKELFEALGRVLVLP 158 6.6679***********************************************9999999******************* PP TIGR00112 159 eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaaklleesgehpalLkdkVtsPgGtTiagl 237 e++++a+ta++G+gPA+vf+++ea+++a+v lG+pr+ea++++ ++++G++kl + sg h +lL+++V+sP+G Tia++ lcl|MicrobesOnline__882:207819 159 EEKFNAFTAVVGCGPAYVFHFMEAVVEAAVTLGFPRHEATDMVVDLFAGSVKLAATSGTHLSLLREAVCSPAGNTIAAM 237 ******************************************************************************* PP TIGR00112 238 avLeekgvrsavieaveaavkrseeL 263 + + +++vr+ +i+a+ aa++r +e+ lcl|MicrobesOnline__882:207819 238 NQFDRDAVRGRIIDAILAAYRRGQEM 263 **********************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (265 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6.29 // [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