Align pyrroline-5-carboxylate reductase (EC 1.5.1.2) (characterized)
to candidate 8502455 DvMF_3161 pyrroline-5-carboxylate reductase (RefSeq)
Query= reanno::Miya:8502455 (269 letters) >FitnessBrowser__Miya:8502455 Length = 269 Score = 522 bits (1344), Expect = e-153 Identities = 269/269 (100%), Positives = 269/269 (100%) Query: 1 MGTVLGCIGCGNMGAAILRGLSGRQGLSLLGYNPTPAKVLALADAGVRAMPDAATLAAQA 60 MGTVLGCIGCGNMGAAILRGLSGRQGLSLLGYNPTPAKVLALADAGVRAMPDAATLAAQA Sbjct: 1 MGTVLGCIGCGNMGAAILRGLSGRQGLSLLGYNPTPAKVLALADAGVRAMPDAATLAAQA 60 Query: 61 DVVLLGVKPYLVPDVLRAIAPSLTPGKVVVSIASGVSIAAMKAAIAEAGGPECPVVRVMP 120 DVVLLGVKPYLVPDVLRAIAPSLTPGKVVVSIASGVSIAAMKAAIAEAGGPECPVVRVMP Sbjct: 61 DVVLLGVKPYLVPDVLRAIAPSLTPGKVVVSIASGVSIAAMKAAIAEAGGPECPVVRVMP 120 Query: 121 NTPAMVGKGVYALCFEDPALDVPRRDLVRGLFESIGTVIVLPEARFTAFTAVVGCGPAYV 180 NTPAMVGKGVYALCFEDPALDVPRRDLVRGLFESIGTVIVLPEARFTAFTAVVGCGPAYV Sbjct: 121 NTPAMVGKGVYALCFEDPALDVPRRDLVRGLFESIGTVIVLPEARFTAFTAVVGCGPAYV 180 Query: 181 FYFMEAVTEVAVTLGFTRQDATELVKGLFSGSVALAEQSGTHLSVLREQVCSPAGNTIAA 240 FYFMEAVTEVAVTLGFTRQDATELVKGLFSGSVALAEQSGTHLSVLREQVCSPAGNTIAA Sbjct: 181 FYFMEAVTEVAVTLGFTRQDATELVKGLFSGSVALAEQSGTHLSVLREQVCSPAGNTIAA 240 Query: 241 MNQLDREAVRGRIMDAVLAAYRRGLEMEK 269 MNQLDREAVRGRIMDAVLAAYRRGLEMEK Sbjct: 241 MNQLDREAVRGRIMDAVLAAYRRGLEMEK 269 Lambda K H 0.322 0.137 0.395 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: 386 Number of extensions: 3 Number of successful extensions: 1 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: 269 Length of database: 269 Length adjustment: 25 Effective length of query: 244 Effective length of database: 244 Effective search space: 59536 Effective search space used: 59536 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 8502455 DvMF_3161 (pyrroline-5-carboxylate reductase (RefSeq))
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.32055.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-76 243.0 0.3 2.3e-76 242.9 0.3 1.0 1 lcl|FitnessBrowser__Miya:8502455 DvMF_3161 pyrroline-5-carboxylat Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Miya:8502455 DvMF_3161 pyrroline-5-carboxylate reductase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 242.9 0.3 2.3e-76 2.3e-76 2 262 .. 6 266 .. 5 267 .. 0.95 Alignments for each domain: == domain 1 score: 242.9 bits; conditional E-value: 2.3e-76 TIGR00112 2 aiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKPqdleevlae 78 + iG+Gnmg+a+l+gl+ ++ ++l +++ ++k+ ala+ +gv+++ da++++++advvll+vKP+ +++vl+ lcl|FitnessBrowser__Miya:8502455 6 GCIGCGNMGAAILRGLSGRQG---LSLLGYNPTPAKVLALAD-AGVRAMPDAATLAAQADVVLLGVKPYLVPDVLRA 78 78*************998744...578889999999988875.679******************************9 PP TIGR00112 79 lkseektkeklliSilAGvtiekleqlleae....krvvRvmPNtaakvgagvtaiaassevsee.qkelveellka 150 ++ + t +k+++Si+ Gv+i++++ ++++ ++vvRvmPNt+a+vg+gv a++ ++++ + +++lv+ l+++ lcl|FitnessBrowser__Miya:8502455 79 IAP-SLTPGKVVVSIASGVSIAAMKAAIAEAggpeCPVVRVMPNTPAMVGKGVYALCFEDPALDVpRRDLVRGLFES 154 999.888*********************8779999*************************999989*********** PP TIGR00112 151 vGkvveveeklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaaklleesgehpalLkdkVt 227 +G+v+ ++e+ + a+ta++G+gPA+vf+++ea+ + +v lG++r+ a+el++ ++ G+++l e+sg h ++L+++V+ lcl|FitnessBrowser__Miya:8502455 155 IGTVIVLPEARFTAFTAVVGCGPAYVFYFMEAVTEVAVTLGFTRQDATELVKGLFSGSVALAEQSGTHLSVLREQVC 231 ***************************************************************************** PP TIGR00112 228 sPgGtTiaglavLeekgvrsavieaveaavkrsee 262 sP+G Tia+++ L +++vr+ +++av aa++r e lcl|FitnessBrowser__Miya:8502455 232 SPAGNTIAAMNQLDREAVRGRIMDAVLAAYRRGLE 266 *******************************9765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (269 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: 00:00:00.00 # Mc/sec: 7.64 // [ok]
This GapMind analysis is from Apr 09 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