Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate Synpcc7942_2058 Synpcc7942_2058 pyrroline-5-carboxylate reductase
Query= SwissProt::Q9HH99 (270 letters) >FitnessBrowser__SynE:Synpcc7942_2058 Length = 264 Score = 205 bits (522), Expect = 7e-58 Identities = 115/263 (43%), Positives = 162/263 (61%), Gaps = 3/263 (1%) Query: 6 IGFIGAGKMGSALMQGTIKAGIVTPENIGASDVYEPFLKDLQAKLGIRVSTDNAVIVRES 65 +G IG G MG AL+ + G V + S+ + + L + G+R DNA ++ Sbjct: 5 LGIIGGGVMGEALLARLLAQGQVAATAVTVSEPFAARCEFLNDRYGVRCVDDNAEAA-QA 63 Query: 66 DILILAVKPQTLSSVLSNLKNEITSEKLVISIAAGVPLSTYEDALLEGTRVVRVMPNIAA 125 D ++LA+KPQ ++ L ++ S++L++SI AGVPL+ E A V+R MPN A Sbjct: 64 DWVLLAIKPQVFDPAVAGLA-DLRSDRLILSILAGVPLAKLE-AAFPHEAVIRAMPNTPA 121 Query: 126 TVSEAASGIAPGKNATPEDLKAALEIFSAVGTAVQVPESLMDAVTGLSGSGPAFIFPVIE 185 TV + IA G+ T + L A E F+AVG V VPES +DAVTGLSGSGP ++ ++E Sbjct: 122 TVGAGVTAIAAGQQVTADQLSQAQEFFAAVGRVVTVPESQLDAVTGLSGSGPGYVALIVE 181 Query: 186 AMADGAVLEGMDRKSALTLAAQTVLGAAKMALETGMHPGELKDMVTSPAGTTIQGIHSLE 245 A++DG V G+ R A LA QTV G A++ ETG HPGELKD V SP GTTI G+ +LE Sbjct: 182 ALSDGGVAAGLPRAIATELAIQTVRGTAELLQETGWHPGELKDRVCSPGGTTIAGVATLE 241 Query: 246 EAGIRAAFMNAVIRASERSKELG 268 + G+R+A + AV A+ RS++LG Sbjct: 242 QNGLRSALIEAVKAAALRSQQLG 264 Lambda K H 0.313 0.130 0.343 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: 193 Number of extensions: 10 Number of successful extensions: 4 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: 270 Length of database: 264 Length adjustment: 25 Effective length of query: 245 Effective length of database: 239 Effective search space: 58555 Effective search space used: 58555 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 47 (22.7 bits)
Align candidate Synpcc7942_2058 Synpcc7942_2058 (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.24506.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-91 292.9 3.1 1.5e-91 292.7 3.1 1.0 1 lcl|FitnessBrowser__SynE:Synpcc7942_2058 Synpcc7942_2058 pyrroline-5-carb Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SynE:Synpcc7942_2058 Synpcc7942_2058 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 292.7 3.1 1.5e-91 1.5e-91 1 263 [] 5 263 .. 5 263 .. 0.98 Alignments for each domain: == domain 1 score: 292.7 bits; conditional E-value: 1.5e-91 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKP 69 ++iiG+G mgeall+ ll++g+ a++ + v e+ +++ + l +++gv+ + d++ea+ +ad+vlla+KP lcl|FitnessBrowser__SynE:Synpcc7942_2058 5 LGIIGGGVMGEALLARLLAQGQVAATAVTVSEPFAARCEFLNDRYGVRCVDDNAEAA-QADWVLLAIKP 72 68**************************************************99888.788******** PP TIGR00112 70 qdleevlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevse 138 q++++++a l++ + ++l++SilAGv+++kle ++++ ++v+R+mPNt+a+vgagvtaiaa+++v++ lcl|FitnessBrowser__SynE:Synpcc7942_2058 73 QVFDPAVAGLAD--LRSDRLILSILAGVPLAKLEAAFPH-EAVIRAMPNTPATVGAGVTAIAAGQQVTA 138 ********9998..5579*******************97.78*************************** PP TIGR00112 139 eqkelveellkavGkvveveeklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkG 207 +q ++++e ++avG vv+v+e++ldavt+lsGSgP +v+l++eal d+gv++GLpr+ a+ela qt+ G lcl|FitnessBrowser__SynE:Synpcc7942_2058 139 DQLSQAQEFFAAVGRVVTVPESQLDAVTGLSGSGPGYVALIVEALSDGGVAAGLPRAIATELAIQTVRG 207 ********************************************************************* PP TIGR00112 208 aaklleesgehpalLkdkVtsPgGtTiaglavLeekgvrsavieaveaavkrseeL 263 +a+ll+e+g hp +Lkd+V+sPgGtTiag+a+Le++g+rsa+ieav+aa+ rs++L lcl|FitnessBrowser__SynE:Synpcc7942_2058 208 TAELLQETGWHPGELKDRVCSPGGTTIAGVATLEQNGLRSALIEAVKAAALRSQQL 263 ******************************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (264 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.29 // [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