Align pyrroline-5-carboxylate reductase (EC 1.5.1.2) (characterized)
to candidate WP_012674059.1 SULAZ_RS08005 pyrroline-5-carboxylate reductase
Query= BRENDA::G7KRM5 (274 letters) >NCBI__GCF_000021545.1:WP_012674059.1 Length = 261 Score = 182 bits (461), Expect = 8e-51 Identities = 107/264 (40%), Positives = 161/264 (60%), Gaps = 5/264 (1%) Query: 11 YTLGFIGAGKMAESIAKGAV-RSGVLSPSRIKTAIHSNPARRTAFESIGITVLSSNDDVV 69 + +G IG G M E+I KG + ++G+ S S + I N R+ S VV Sbjct: 2 FKVGVIGCGNMGEAIIKGLIEKAGINSTSIVVNDI--NKERQNYIVEKYNVAGSDIRKVV 59 Query: 70 RDSNVVVFSVKPQLLKDVVLKLKPLLTKDKLLVSVAAGIKMKDLQEWAGHERFIRVMPNT 129 S +V VKP+ L+D + +K L ++++L+SV AG+K++ ++ +R+MPNT Sbjct: 60 NLSEIVFLVVKPKDLQDSLESIKDLFKENQILISVLAGVKIEKIKSIVEKPLVVRIMPNT 119 Query: 130 AATVGEAASVMSLGGAATEEDANLISQLFGSIGKIWKADDKYFDAITGLSGSGPAYIYLA 189 A +GE +S TE+ +I L G +G++++ ++ D ITGLSGSGPAY++ Sbjct: 120 PALIGEGVIGVSFE-KDTEKKQEIIDLLKG-LGEVFEVKEELLDVITGLSGSGPAYVFTF 177 Query: 190 IEALADGGVAAGLPRDLALSLASQTVLGAASMATQSGKHPGQLKDDVTSPGGTTIAGVHE 249 I+ALA GGV GLP AL +A+QTVLGAA + ++G+HP L+D V+SP GTTI G+HE Sbjct: 178 IDALAQGGVKMGLPYQDALKIATQTVLGAAKLLKETGEHPAVLRDTVSSPAGTTIYGLHE 237 Query: 250 LEKAGFRGILMNAVVAAAKRSQEL 273 LEK F+ +++AV A KRS+EL Sbjct: 238 LEKKNFKDAVISAVETATKRSKEL 261 Lambda K H 0.315 0.131 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: 152 Number of extensions: 5 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: 274 Length of database: 261 Length adjustment: 25 Effective length of query: 249 Effective length of database: 236 Effective search space: 58764 Effective search space used: 58764 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_012674059.1 SULAZ_RS08005 (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.5564.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-91 291.3 0.8 4.5e-91 291.1 0.8 1.0 1 lcl|NCBI__GCF_000021545.1:WP_012674059.1 SULAZ_RS08005 pyrroline-5-carbox Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021545.1:WP_012674059.1 SULAZ_RS08005 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 291.1 0.8 4.5e-91 4.5e-91 1 263 [] 4 261 .] 4 261 .] 0.96 Alignments for each domain: == domain 1 score: 291.1 bits; conditional E-value: 4.5e-91 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKP 69 +++iG+Gnmgea+++gl++k+ +++++i+v + ++e+ ++ +++++v+ + +++v+ +++v+l vKP lcl|NCBI__GCF_000021545.1:WP_012674059.1 4 VGVIGCGNMGEAIIKGLIEKAGINSTSIVVNDINKERQNYIVEKYNVAGSDI-RKVVNLSEIVFLVVKP 71 689********************99999999999***********9887666.7899************ PP TIGR00112 70 qdleevlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevse 138 +dl++ l+++k+ +++++liS+lAGv+iek+++ +e+ vvR+mPNt+a +g+gv++++ ++++ lcl|NCBI__GCF_000021545.1:WP_012674059.1 72 KDLQDSLESIKD-LFKENQILISVLAGVKIEKIKSIVEK-PLVVRIMPNTPALIGEGVIGVSFEKDT-- 136 ***********9.55589*******************85.88**********************654.. PP TIGR00112 139 eqkelveellkavGkvveveeklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkG 207 e+k+++ +llk +G+v ev+e+lld +t+lsGSgPA+vf++i+ala++gvk+GLp + a+++a+qt+ G lcl|NCBI__GCF_000021545.1:WP_012674059.1 137 EKKQEIIDLLKGLGEVFEVKEELLDVITGLSGSGPAYVFTFIDALAQGGVKMGLPYQDALKIATQTVLG 205 56789**************************************************************** PP TIGR00112 208 aaklleesgehpalLkdkVtsPgGtTiaglavLeekgvrsavieaveaavkrseeL 263 aakll+e+gehpa+L+d V+sP+GtTi gl++Le+k++++avi ave a+krs+eL lcl|NCBI__GCF_000021545.1:WP_012674059.1 206 AAKLLKETGEHPAVLRDTVSSPAGTTIYGLHELEKKNFKDAVISAVETATKRSKEL 261 ******************************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (261 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: 5.81 // [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