Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate WP_011382988.1 AMB_RS02820 pyrroline-5-carboxylate reductase
Query= SwissProt::P22008 (273 letters) >NCBI__GCF_000009985.1:WP_011382988.1 Length = 263 Score = 155 bits (393), Expect = 6e-43 Identities = 106/269 (39%), Positives = 141/269 (52%), Gaps = 14/269 (5%) Query: 5 RIAFIGAGNMAASLIGGLRAQGVPAAQIRASDPGAEQRAKIAGEFAIDVVESNAEAVADA 64 +I +G G M ++++ G +GV + DP + A+ VV S+A A+ A Sbjct: 3 KILLVGCGKMGSAMLAGWLERGVAPGDVVVVDPSSPDLG------AVGVVTSDA-AIPSA 55 Query: 65 ---DVVVLSVKPQAMKAVCQALAPALKPEQLIVSIAAGIPCASLEAWLGQPRPVVRCMPN 121 DVV+ +VKPQ M V A + +SIAAG A LG +VR MPN Sbjct: 56 FVPDVVIFAVKPQVMAEVVPPYARF--DRSVFLSIAAGKTIAFFRNHLGAKAVIVRAMPN 113 Query: 122 TPALLRQGASGLYANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGPAYFF 181 TPA +R+G + A V A E LL AVG W+DDE +D VTAVSGSGPAY F Sbjct: 114 TPAAVRRGITVCCAGEAVPAVARELCQSLLEAVGEVGWVDDEGLMDVVTAVSGSGPAYIF 173 Query: 182 LLMQAMTDAGEKLGLSRETASRLTLQTALGAAQMALSSEVEPAELRRRVTSPNGTTEAAI 241 LL +AM AG GL A RL T GA ++ S +LR+ VTSP GTT AA+ Sbjct: 174 LLAEAMEAAGLAQGLPPALAERLARATVAGAGELLRLSAESAEQLRKNVTSPGGTTAAAL 233 Query: 242 KSFQA--NGFEALVEQALNAASQRSAELA 268 A +G +L+ +A+ AA++R ELA Sbjct: 234 SVLMAESHGIPSLMTEAVAAATRRGRELA 262 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: 198 Number of extensions: 8 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: 273 Length of database: 263 Length adjustment: 25 Effective length of query: 248 Effective length of database: 238 Effective search space: 59024 Effective search space used: 59024 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_011382988.1 AMB_RS02820 (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.4106.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-75 239.7 2.3 2.4e-75 239.5 2.3 1.0 1 lcl|NCBI__GCF_000009985.1:WP_011382988.1 AMB_RS02820 pyrroline-5-carboxyl Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_011382988.1 AMB_RS02820 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 239.5 2.3 2.4e-75 2.4e-75 1 263 [] 4 261 .. 4 261 .. 0.92 Alignments for each domain: == domain 1 score: 239.5 bits; conditional E-value: 2.4e-75 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKP 69 i ++G+G+mg+a+l+g+l++g++ + +++v+++s++ l a gv ++ +a + dvv++avKP lcl|NCBI__GCF_000009985.1:WP_011382988.1 4 ILLVGCGKMGSAMLAGWLERGVA-PGDVVVVDPSSPDLGAV----GVVTSDAAIPSAFVPDVVIFAVKP 67 679****************9887.89*****9887766654....4444444444455789******** PP TIGR00112 70 qdleevlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevse 138 q++ ev+ ++ ++++Si+AG ti+ ++++l+a++ +vR+mPNt+a+v++g+t+ +a+++v + lcl|NCBI__GCF_000009985.1:WP_011382988.1 68 QVMAEVVPPYAR---FDRSVFLSIAAGKTIAFFRNHLGAKAVIVRAMPNTPAAVRRGITVCCAGEAVPA 133 ********9988...5679*********************************************99988 PP TIGR00112 139 eqkelveellkavGkvveve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlk 206 +el ++ll+avG+v +v+ e l+d vta+sGSgPA++fll+ea+++ag+++GLp ++a++la++t++ lcl|NCBI__GCF_000009985.1:WP_011382988.1 134 VARELCQSLLEAVGEVGWVDdEGLMDVVTAVSGSGPAYIFLLAEAMEAAGLAQGLPPALAERLARATVA 202 8*******************9************************************************ PP TIGR00112 207 GaaklleesgehpalLkdkVtsPgGtTiaglavL..eekgvrsavieaveaavkrseeL 263 Ga++ll s e++++L+++VtsPgGtT+a+l+vL e +g+ s + eav aa++r +eL lcl|NCBI__GCF_000009985.1:WP_011382988.1 203 GAGELLRLSAESAEQLRKNVTSPGGTTAAALSVLmaESHGIPSLMTEAVAAATRRGREL 261 **********************************3334679**************9997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (263 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: 8.02 // [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