Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate Ga0059261_3321 Ga0059261_3321 pyrroline-5-carboxylate reductase
Query= SwissProt::P22008 (273 letters) >FitnessBrowser__Korea:Ga0059261_3321 Length = 258 Score = 158 bits (399), Expect = 1e-43 Identities = 107/266 (40%), Positives = 143/266 (53%), Gaps = 14/266 (5%) Query: 6 IAFIGAGNMAASLIGGLRAQGVPAA-QIRASDPGAEQRAKIAGEF-AIDVVESNAEAVAD 63 + +G G M GG A+G A ++ DP A + + ++D VE+ E Sbjct: 3 VLLVGCGRM-----GGAMARGWNGAHRVLVFDPMAAELPEGTERVDSLDDVEAGGEMA-- 55 Query: 64 ADVVVLSVKPQAMKAVCQALAPALKPEQLIVSIAAGIPCASLEAWLGQPRPVVRCMPNTP 123 VVL+VKPQ ++ ++L P + + L VSI AGI L LG R VR MPNTP Sbjct: 56 ---VVLAVKPQVFPSIGESLRPLARHDALFVSIMAGITLQGLSDALGSGR-TVRTMPNTP 111 Query: 124 ALLRQGASGLYANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGPAYFFLL 183 A + QG + A V +LL G +W+D+EAQIDAVTAVSGSGPAYFF Sbjct: 112 AAIGQGITAAVAGRDVRMGDFATVNELLGPTGQVVWIDEEAQIDAVTAVSGSGPAYFFRF 171 Query: 184 MQAMTDAGEKLGLSRETASRLTLQTALGAAQMALSSEVEPAELRRRVTSPNGTTEAAIKS 243 +A+ AG + GL E A +L T GAA +A + E AELRR+VTSP GTT A + Sbjct: 172 TEALARAGAEEGLPPELAMQLARATFTGAAALAGADPAELAELRRQVTSPGGTTAAGLGQ 231 Query: 244 F-QANGFEALVEQALNAASQRSAELA 268 + + LV + + AA+ RS ELA Sbjct: 232 LDHDDAIDRLVRKVVEAAAARSRELA 257 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: 186 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: 258 Length adjustment: 25 Effective length of query: 248 Effective length of database: 233 Effective search space: 57784 Effective search space used: 57784 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 Ga0059261_3321 Ga0059261_3321 (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.carbon/TIGR00112.hmm # target sequence database: /tmp/gapView.7356.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-70 224.0 0.2 1.6e-70 223.8 0.2 1.0 1 lcl|FitnessBrowser__Korea:Ga0059261_3321 Ga0059261_3321 pyrroline-5-carbo Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Korea:Ga0059261_3321 Ga0059261_3321 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 223.8 0.2 1.6e-70 1.6e-70 2 263 .] 4 256 .. 3 256 .. 0.93 Alignments for each domain: == domain 1 score: 223.8 bits; conditional E-value: 1.6e-70 TIGR00112 2 aiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKPq 70 ++G+G+mg a+++g+ + +++lv ++++++l + +++ + d++ea e+ v+lavKPq lcl|FitnessBrowser__Korea:Ga0059261_3321 4 LLVGCGRMGGAMARGWNGA-----HRVLVFDPMAAELPEGTERV---DSLDDVEAGGEM-AVVLAVKPQ 63 689************9886.....56899998888777776665...444556778777.89******* PP TIGR00112 71 dleevlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevsee 139 +++++ ++l+ +++++l++Si+AG+t++ l+++l++ r+vR mPNt+a++g+g+ta++a+++v+ lcl|FitnessBrowser__Korea:Ga0059261_3321 64 VFPSIGESLRP-LARHDALFVSIMAGITLQGLSDALGS-GRTVRTMPNTPAAIGQGITAAVAGRDVRMG 130 **********9.6669********************86.78**************************** PP TIGR00112 140 qkelveellkavGkvveve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkG 207 + ++v+ell +G+vv+++ e+++davta+sGSgPA++f + eala+ag ++GLp e+a++la++t+ G lcl|FitnessBrowser__Korea:Ga0059261_3321 131 DFATVNELLGPTGQVVWIDeEAQIDAVTAVSGSGPAYFFRFTEALARAGAEEGLPPELAMQLARATFTG 199 *******************99************************************************ PP TIGR00112 208 aaklleesgehpalLkdkVtsPgGtTiaglavLeekg.vrsavieaveaavkrseeL 263 aa+l + a+L+ +VtsPgGtT+agl L +++ + + v + veaa++rs+eL lcl|FitnessBrowser__Korea:Ga0059261_3321 200 AAALAGADPAELAELRRQVTSPGGTTAAGLGQLDHDDaIDRLVRKVVEAAAARSREL 256 *********************************99886999*************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (258 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: 7.22 // [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