Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate WP_028314493.1 G491_RS0109980 pyrroline-5-carboxylate reductase
Query= SwissProt::Q9HH99 (270 letters) >NCBI__GCF_000429905.1:WP_028314493.1 Length = 281 Score = 179 bits (454), Expect = 6e-50 Identities = 112/278 (40%), Positives = 155/278 (55%), Gaps = 12/278 (4%) Query: 3 NQKIGFIGAGKMGSALMQGTIKAGIVTPENIGASDVYEPFLKDLQAKLGIRVSTDNAVIV 62 N IGFIGAG M A++ +K+ ++ P+NI ASD+ L+ + + GI + DNA + Sbjct: 4 NLSIGFIGAGNMAWAIIGALVKSEVLPPKNIIASDITAERLELAEKEFGIITTQDNAQVF 63 Query: 63 RESDILILAVKPQTLSSVLSNL--KNEITSE--KLVISIAAGVPLSTYEDALLEGTR--- 115 +S+ ++LAVKPQ L VL NL E E KL+ISIAAGV + E L G Sbjct: 64 AKSNAVVLAVKPQFLPEVLENLVASPEFPGEGRKLIISIAAGVGCAKMEGILYAGLDEEA 123 Query: 116 -----VVRVMPNIAATVSEAASGIAPGKNATPEDLKAALEIFSAVGTAVQVPESLMDAVT 170 +VRVMPN A V + +G+AP A ED + A I A G A+ E ++ VT Sbjct: 124 KSRLPIVRVMPNTPALVGQGMAGMAPNAYALEEDRQTAQTIMDAAGKALWFDEKDINGVT 183 Query: 171 GLSGSGPAFIFPVIEAMADGAVLEGMDRKSALTLAAQTVLGAAKMALETGMHPGELKDMV 230 LSGSGPA++F + EAM G V G+ AL +A QT+ GAA + ETG PG L+ V Sbjct: 184 ALSGSGPAYVFYLAEAMVQGGVEVGLPEDKALEMAIQTIKGAALLMEETGEAPGLLRQKV 243 Query: 231 TSPAGTTIQGIHSLEEAGIRAAFMNAVIRASERSKELG 268 TS GTT ++ E + A + ++ A +R +ELG Sbjct: 244 TSKGGTTAAALNVFNENKVLEAIVKGMLAAKKRGEELG 281 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: 207 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: 270 Length of database: 281 Length adjustment: 25 Effective length of query: 245 Effective length of database: 256 Effective search space: 62720 Effective search space used: 62720 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 WP_028314493.1 G491_RS0109980 (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.21627.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-80 256.2 4.4 2.3e-80 256.0 4.4 1.0 1 lcl|NCBI__GCF_000429905.1:WP_028314493.1 G491_RS0109980 pyrroline-5-carbo Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000429905.1:WP_028314493.1 G491_RS0109980 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 256.0 4.4 2.3e-80 2.3e-80 1 263 [] 7 280 .. 7 280 .. 0.97 Alignments for each domain: == domain 1 score: 256.0 bits; conditional E-value: 2.3e-80 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKP 69 i++iGaGnm+ a++ +l+k+++ +k+i+ + +e+l+ ke+g+ +t+d++++ ++++ v+lavKP lcl|NCBI__GCF_000429905.1:WP_028314493.1 7 IGFIGAGNMAWAIIGALVKSEVLPPKNIIASDITAERLELAEKEFGIITTQDNAQVFAKSNAVVLAVKP 75 89*********************99999999999*********************************** PP TIGR00112 70 qdleevlaelks...eektkeklliSilAGvtiekleqlleae........krvvRvmPNtaakvgagv 127 q l+evl++l + kl+iSi+AGv ++k+e l+a ++vRvmPNt+a vg+g+ lcl|NCBI__GCF_000429905.1:WP_028314493.1 76 QFLPEVLENLVAspeFPGEGRKLIISIAAGVGCAKMEGILYAGldeeaksrLPIVRVMPNTPALVGQGM 144 *********9986654456789******************9989999*99999**************** PP TIGR00112 128 taiaassevseeqkelveellkavGkvveveeklldavtalsGSgPAfvflliealadagvklGLpree 196 +++a ++++ ee++++++ +++a Gk+++ +ek+++ vtalsGSgPA+vf+l+ea++++gv++GLp+++ lcl|NCBI__GCF_000429905.1:WP_028314493.1 145 AGMAPNAYALEEDRQTAQTIMDAAGKALWFDEKDINGVTALSGSGPAYVFYLAEAMVQGGVEVGLPEDK 213 ********************************************************************* PP TIGR00112 197 akelaaqtlkGaaklleesgehpalLkdkVtsPgGtTiaglavLeekgvrsavieaveaavkrseeL 263 a+e+a qt+kGaa l+ee+ge p lL++kVts+gGtT+a+l+v++e++v +a+ +++ aa+kr eeL lcl|NCBI__GCF_000429905.1:WP_028314493.1 214 ALEMAIQTIKGAALLMEETGEAPGLLRQKVTSKGGTTAAALNVFNENKVLEAIVKGMLAAKKRGEEL 280 ***************************************************************9997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (281 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: 00:00:00.01 # Mc/sec: 6.56 // [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