Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate WP_034995200.1 DL88_RS09545 pyrroline-5-carboxylate reductase
Query= SwissProt::P22008 (273 letters) >NCBI__GCF_000745425.1:WP_034995200.1 Length = 275 Score = 160 bits (404), Expect = 4e-44 Identities = 102/261 (39%), Positives = 142/261 (54%), Gaps = 5/261 (1%) Query: 10 GAGNMAASLIGGLRAQGVPAAQIRASDPGAEQRAKIAGEFAIDVVESNAEAVADADVVVL 69 GAG M ++L+ + G+P A I DP + A+ + A A V++L Sbjct: 17 GAGKMGSALLESWLSLGLPGANIGVIDP---HPSPALSALAVQHGLTLAPHPLIAQVLLL 73 Query: 70 SVKPQAMKAVCQALAPALKPEQLIVSIAAGIPCASLEAWLGQPRPVVRCMPNTPALLRQG 129 ++KPQ + AL + LI+SI AG A+L +VR MPN PA + G Sbjct: 74 AIKPQMLDKAAPALQHYVDGRTLIISILAGKTIATLRHHFPHAGAIVRAMPNLPASIGLG 133 Query: 130 ASGLYANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGPAYFFLLMQAMTD 189 +G A +++ Q A LL A G WLDDEA IDAVTA+SGSGPAY F ++ ++ Sbjct: 134 ITGAVAGPELTQEQQAFATTLLGAAGSVEWLDDEALIDAVTAISGSGPAYVFYFVECLSQ 193 Query: 190 AGEKLGLSRETASRLTLQTALGAAQMAL-SSEVEPAELRRRVTSPNGTTEAAIKSFQA-N 247 AG LGL ++ + RL T GA + + + + PA+LR VTSP GTT AA++ A N Sbjct: 194 AGVALGLPQDISERLARATVEGAGGLLMHETGIRPAQLRENVTSPGGTTAAALEVLMAQN 253 Query: 248 GFEALVEQALNAASQRSAELA 268 G L+EQA AA +R+AELA Sbjct: 254 GLAPLMEQAAQAARKRAAELA 274 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: 9 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: 273 Length of database: 275 Length adjustment: 25 Effective length of query: 248 Effective length of database: 250 Effective search space: 62000 Effective search space used: 62000 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_034995200.1 DL88_RS09545 (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.30887.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-73 233.7 1.3 1.7e-73 233.5 1.3 1.0 1 lcl|NCBI__GCF_000745425.1:WP_034995200.1 DL88_RS09545 pyrroline-5-carboxy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000745425.1:WP_034995200.1 DL88_RS09545 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 233.5 1.3 1.7e-73 1.7e-73 3 263 .] 15 273 .. 13 273 .. 0.93 Alignments for each domain: == domain 1 score: 233.5 bits; conditional E-value: 1.7e-73 TIGR00112 3 iiGaGnmgeallsgllkkgakakkeilviers.eeklaalakelgvevtsdaeeavkeadvvllavKPq 70 + GaG+mg+all+++l+ g + ++i vi+++ +++l ala + g + + + ++ a+v+lla+KPq lcl|NCBI__GCF_000745425.1:WP_034995200.1 15 LAGAGKMGSALLESWLSLGLP-GANIGVIDPHpSPALSALAVQHGLTLAPHP--LI--AQVLLLAIKPQ 78 67***************9887.89********77888888888887777664..44..569******** PP TIGR00112 71 dleevlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevsee 139 +l++++ l++ +l+iSilAG ti++l++++++ ++vR+mPN++a++g g+t+++a+ e ++e lcl|NCBI__GCF_000745425.1:WP_034995200.1 79 MLDKAAPALQH-YVDGRTLIISILAGKTIATLRHHFPHAGAIVRAMPNLPASIGLGITGAVAGPELTQE 146 ********998.66689**************************************************** PP TIGR00112 140 qkelveellkavGkvveve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkG 207 q++ ++ ll a G+v +++ e+l+davta+sGSgPA+vf+++e+l +agv+lGLp++ +++la++t++G lcl|NCBI__GCF_000745425.1:WP_034995200.1 147 QQAFATTLLGAAGSVEWLDdEALIDAVTAISGSGPAYVFYFVECLSQAGVALGLPQDISERLARATVEG 215 ********************************************************************* PP TIGR00112 208 aaklleesge.hpalLkdkVtsPgGtTiaglavLeekg.vrsavieaveaavkrseeL 263 a+ ll+++++ +pa+L+++VtsPgGtT+a+l+vL++++ + +++a +aa kr+ eL lcl|NCBI__GCF_000745425.1:WP_034995200.1 216 AGGLLMHETGiRPAQLRENVTSPGGTTAAALEVLMAQNgLAPLMEQAAQAARKRAAEL 273 ***99877667**********************986544999*************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (275 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: 7.40 // [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