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.23309.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 9.64 // [ok]
This GapMind analysis is from Apr 09 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