Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate WP_066922652.1 ACG33_RS01405 pyrroline-5-carboxylate reductase
Query= SwissProt::P22008 (273 letters) >NCBI__GCF_001579945.1:WP_066922652.1 Length = 273 Score = 239 bits (609), Expect = 6e-68 Identities = 130/267 (48%), Positives = 178/267 (66%), Gaps = 2/267 (0%) Query: 6 IAFIGAGNMAASLIGGLRAQGVPAAQIRASDPGAEQRAKIAGEFAIDVVESNAEAVADAD 65 +AFIG GNMAASLIGGL A+G+PA +I +D EQ + F I SN A A+AD Sbjct: 6 LAFIGGGNMAASLIGGLIARGMPAGRIIVADRVPEQLQALRTRFGIRTTSSNPAAAAEAD 65 Query: 66 VVVLSVKPQAMKAVCQALAPAL-KPEQLIVSIAAGIPCASLEAWLGQPRPVVRCMPNTPA 124 V+ +VKPQ + +V L L + L++SIAAG+ L+ W+G PVVRCMPN PA Sbjct: 66 TVLFAVKPQDLASVSAELRDVLARRRPLLISIAAGVHSRDLQRWVGG-LPVVRCMPNRPA 124 Query: 125 LLRQGASGLYANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGPAYFFLLM 184 + G +G+YA +V+A Q E A Q+L AVG LWL+ E +DAVTA+SGSGPAYFFLL+ Sbjct: 125 MQGCGVTGMYATHEVAATQRELAEQVLGAVGTVLWLEREEDLDAVTAISGSGPAYFFLLI 184 Query: 185 QAMTDAGEKLGLSRETASRLTLQTALGAAQMALSSEVEPAELRRRVTSPNGTTEAAIKSF 244 +++ AG+ LGL E + +L ++TA GA+ MA + A LR +VTS GTTEAA+K Sbjct: 185 ESLQQAGQSLGLPEEISRKLAIETAYGASMMARVARESAATLREQVTSKGGTTEAALKHL 244 Query: 245 QANGFEALVEQALNAASQRSAELAEQL 271 +A+ F ++ A+ AA++RSA+LAE+L Sbjct: 245 EASDFRGIMATAVAAAARRSAQLAEEL 271 Lambda K H 0.315 0.127 0.348 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: 7 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: 273 Length of database: 273 Length adjustment: 25 Effective length of query: 248 Effective length of database: 248 Effective search space: 61504 Effective search space used: 61504 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_066922652.1 ACG33_RS01405 (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.25256.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.1e-82 261.7 2.7 4.6e-82 261.6 2.7 1.0 1 lcl|NCBI__GCF_001579945.1:WP_066922652.1 ACG33_RS01405 pyrroline-5-carbox Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001579945.1:WP_066922652.1 ACG33_RS01405 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 261.6 2.7 4.6e-82 4.6e-82 1 263 [] 6 267 .. 6 267 .. 0.99 Alignments for each domain: == domain 1 score: 261.6 bits; conditional E-value: 4.6e-82 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKP 69 +a+iG+Gnm+++l+ gl+++g + + +i+v++r +e+l+al +++g+++ts++ +a++ead+vl+avKP lcl|NCBI__GCF_001579945.1:WP_066922652.1 6 LAFIGGGNMAASLIGGLIARGMP-AGRIIVADRVPEQLQALRTRFGIRTTSSNPAAAAEADTVLFAVKP 73 69******************988.89******************************************* PP TIGR00112 70 qdleevlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevse 138 qdl +v ael++ +++ lliSi+AGv+ +l++++++ +vvR+mPN +a+ g gvt+++a++ev + lcl|NCBI__GCF_001579945.1:WP_066922652.1 74 QDLASVSAELRDVLARRRPLLISIAAGVHSRDLQRWVGG-LPVVRCMPNRPAMQGCGVTGMYATHEVAA 141 ************9999*********************86.9**************************** PP TIGR00112 139 eqkelveellkavGkvveve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlk 206 +q+el+e++l avG+v+++e e++ldavta+sGSgPA++fllie+l++ag lGLp+e +++la +t lcl|NCBI__GCF_001579945.1:WP_066922652.1 142 TQRELAEQVLGAVGTVLWLErEEDLDAVTAISGSGPAYFFLLIESLQQAGQSLGLPEEISRKLAIETAY 210 ********************************************************************* PP TIGR00112 207 GaaklleesgehpalLkdkVtsPgGtTiaglavLeekgvrsavieaveaavkrseeL 263 Ga+ + +e++a+L+++Vts+gGtT a+l+ Le++++r+ ++ av aa++rs +L lcl|NCBI__GCF_001579945.1:WP_066922652.1 211 GASMMARVARESAATLREQVTSKGGTTEAALKHLEASDFRGIMATAVAAAARRSAQL 267 ******************************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (273 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.37 // [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