Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate HSERO_RS18990 HSERO_RS18990 pyrroline-5-carboxylate reductase
Query= SwissProt::P22008 (273 letters) >FitnessBrowser__HerbieS:HSERO_RS18990 Length = 260 Score = 208 bits (529), Expect = 1e-58 Identities = 123/260 (47%), Positives = 157/260 (60%), Gaps = 1/260 (0%) Query: 14 MAASLIGGLRAQGVPAAQIRASDPGAEQRAKIAGEFAIDVVESNAEAVADADVVVLSVKP 73 MAA+LIGGL + A I D A+ A + F + V + A+A ADVVVL+VKP Sbjct: 1 MAAALIGGLVGKVAAAQDIHVVDLNAQALASLKDRFGVSVAPAMDGALASADVVVLAVKP 60 Query: 74 QAMKAVCQALAPALKPEQLIVSIAAGIPCASLEAWLGQPRPVVRCMPNTPALLRQGASGL 133 Q M+ V +L P + QL+VSIAAGI L WL +VR MPNTPAL+ +G +GL Sbjct: 61 QQMRDVVGSLKPFIGA-QLVVSIAAGIRMVDLSRWLDGHEAIVRAMPNTPALIGKGITGL 119 Query: 134 YANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGPAYFFLLMQAMTDAGEK 193 + +VS Q QA +L AVG LWL DEAQIDAVTAVSGSGPAY F ++AM A + Sbjct: 120 VPHEKVSTLQRAQADSILKAVGQTLWLSDEAQIDAVTAVSGSGPAYVFYFLEAMEQAAAQ 179 Query: 194 LGLSRETASRLTLQTALGAAQMALSSEVEPAELRRRVTSPNGTTEAAIKSFQANGFEALV 253 LGLS L T GA ++A SE A LR RVTS GTT AA+ S + +G + + Sbjct: 180 LGLSPAEGLELAKATFEGATELARRSEESVATLRERVTSKGGTTYAALTSLEQSGVKDAI 239 Query: 254 EQALNAASQRSAELAEQLGQ 273 +AL AA+ RS EL ++ G+ Sbjct: 240 VKALQAAAVRSKELGDEFGK 259 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: 183 Number of extensions: 6 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: 260 Length adjustment: 25 Effective length of query: 248 Effective length of database: 235 Effective search space: 58280 Effective search space used: 58280 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 HSERO_RS18990 HSERO_RS18990 (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.11529.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-78 249.9 7.5 1.9e-78 249.7 7.5 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS18990 HSERO_RS18990 pyrroline-5-carbox Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS18990 HSERO_RS18990 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 249.7 7.5 1.9e-78 1.9e-78 9 263 .] 1 253 [. 1 253 [. 0.98 Alignments for each domain: == domain 1 score: 249.7 bits; conditional E-value: 1.9e-78 TIGR00112 9 mgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKPqdleevl 76 m++al+ gl+ k ++a+++i+v++ ++++la l +++gv+v+ + + a + advv+lavKPq++++v+ lcl|FitnessBrowser__HerbieS:HSERO_RS18990 1 MAAALIGGLVGK-VAAAQDIHVVDLNAQALASLKDRFGVSVAPAMDGALASADVVVLAVKPQQMRDVV 67 9**********8.5569*************************************************** PP TIGR00112 77 aelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevseeqkelv 144 +lk + ++l++Si+AG+++ +l+++l++++++vR+mPNt+a +g+g+t+++ +++vs q++++ lcl|FitnessBrowser__HerbieS:HSERO_RS18990 68 GSLKP--FIGAQLVVSIAAGIRMVDLSRWLDGHEAIVRAMPNTPALIGKGITGLVPHEKVSTLQRAQA 133 ****9..6689*************************************************999***** PP TIGR00112 145 eellkavGkvveve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaakl 211 +++lkavG++++++ e+++davta+sGSgPA+vf+++ea+++a+ +lGL+ +e +ela++t++Ga +l lcl|FitnessBrowser__HerbieS:HSERO_RS18990 134 DSILKAVGQTLWLSdEAQIDAVTAVSGSGPAYVFYFLEAMEQAAAQLGLSPAEGLELAKATFEGATEL 201 **************9***************************************************** PP TIGR00112 212 leesgehpalLkdkVtsPgGtTiaglavLeekgvrsavieaveaavkrseeL 263 +s+e+ a+L+++Vts+gGtT a+l +Le++gv++a+ +a++aa+ rs+eL lcl|FitnessBrowser__HerbieS:HSERO_RS18990 202 ARRSEESVATLRERVTSKGGTTYAALTSLEQSGVKDAIVKALQAAAVRSKEL 253 **************************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (260 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 8.22 // [ok]
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.
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