Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate PfGW456L13_1010 Pyrroline-5-carboxylate reductase (EC 1.5.1.2)
Query= SwissProt::P22008 (273 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1010 Length = 272 Score = 385 bits (990), Expect = e-112 Identities = 201/273 (73%), Positives = 236/273 (86%), Gaps = 1/273 (0%) Query: 1 MSTPRIAFIGAGNMAASLIGGLRAQGVPAAQIRASDPGAEQRAKIAGEFAIDVVESNAEA 60 MS RIAFIGAGNMAASLIGGLRA+G+ AAQIRASDPG E RA+++ E I+ NA+A Sbjct: 1 MSKTRIAFIGAGNMAASLIGGLRAKGLEAAQIRASDPGEETRARVSAEHGIETFADNAQA 60 Query: 61 VADADVVVLSVKPQAMKAVCQALAPALKPEQLIVSIAAGIPCASLEAWLGQPRPVVRCMP 120 + ADVVVL+VKPQAMKAVC+A+ P+LKP QL+VSIAAGI CAS+ WLG +P+VRCMP Sbjct: 61 IDGADVVVLAVKPQAMKAVCEAIRPSLKPHQLVVSIAAGITCASMNNWLGA-QPIVRCMP 119 Query: 121 NTPALLRQGASGLYANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGPAYF 180 NTPAL+RQGASGL+A +VSA Q +QA +LLSAVGIALWL++E Q+DAVTAVSGSGPAYF Sbjct: 120 NTPALVRQGASGLFATTEVSAEQRQQAQELLSAVGIALWLNEEQQLDAVTAVSGSGPAYF 179 Query: 181 FLLMQAMTDAGEKLGLSRETASRLTLQTALGAAQMALSSEVEPAELRRRVTSPNGTTEAA 240 FLL++AMT AG KLGL + A++LTLQTALGAA MA+SS+V+ AELRRRVTSP GTTEAA Sbjct: 180 FLLIEAMTAAGVKLGLPADIAAQLTLQTALGAAHMAVSSDVDAAELRRRVTSPAGTTEAA 239 Query: 241 IKSFQANGFEALVEQALNAASQRSAELAEQLGQ 273 IKSFQANGFEALVE+AL AA+ RSAE+AEQLGQ Sbjct: 240 IKSFQANGFEALVEKALGAAAHRSAEMAEQLGQ 272 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: 278 Number of extensions: 7 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: 272 Length adjustment: 25 Effective length of query: 248 Effective length of database: 247 Effective search space: 61256 Effective search space used: 61256 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 PfGW456L13_1010 (Pyrroline-5-carboxylate reductase (EC 1.5.1.2))
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.21194.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.6e-82 260.9 10.0 8.5e-82 260.7 10.0 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1010 Pyrroline-5-carboxylate reductas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1010 Pyrroline-5-carboxylate reductase (EC 1.5.1.2) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 260.7 10.0 8.5e-82 8.5e-82 1 263 [] 6 266 .. 6 266 .. 0.98 Alignments for each domain: == domain 1 score: 260.7 bits; conditional E-value: 8.5e-82 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaee 55 ia+iGaGnm+++l+ gl +kg +++i ++ ee +a+ +e g+e+ +d+++ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1010 6 IAFIGAGNMAASLIGGLRAKGLE-AAQIRASDPGEETRARVSAEHGIETFADNAQ 59 89**************9999776.8****************************** PP TIGR00112 56 avkeadvvllavKPqdleevlaelkseektkeklliSilAGvtiekleqlleaek 110 a++ advv+lavKPq +++v++ ++ + + ++l++Si+AG+t++ ++++l+a + lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1010 60 AIDGADVVVLAVKPQAMKAVCEAIRP-SLKPHQLVVSIAAGITCASMNNWLGA-Q 112 **********************9998.6669********************86.9 PP TIGR00112 111 rvvRvmPNtaakvgagvtaiaassevseeqkelveellkavGkvveve.ekllda 164 ++vR+mPNt+a v++g+++++a++evs+eq+++++ell+avG +++++ e++lda lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1010 113 PIVRCMPNTPALVRQGASGLFATTEVSAEQRQQAQELLSAVGIALWLNeEQQLDA 167 9***********************************************99***** PP TIGR00112 165 vtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaaklleesgehp 219 vta+sGSgPA++flliea+ +agvklGLp++ a +l+ qt Gaa++ s+ ++ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1010 168 VTAVSGSGPAYFFLLIEAMTAAGVKLGLPADIAAQLTLQTALGAAHMAVSSDVDA 222 ******************************************************* PP TIGR00112 220 alLkdkVtsPgGtTiaglavLeekgvrsavieaveaavkrseeL 263 a+L+ +VtsP+GtT a++++++++g+++ v++a+ aa++rs e+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1010 223 AELRRRVTSPAGTTEAAIKSFQANGFEALVEKALGAAAHRSAEM 266 ****************************************9885 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (272 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: 9.42 // [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