Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate AO353_08165 AO353_08165 pyrroline-5-carboxylate reductase
Query= SwissProt::P22008 (273 letters) >FitnessBrowser__pseudo3_N2E3:AO353_08165 Length = 272 Score = 388 bits (996), Expect = e-113 Identities = 202/273 (73%), Positives = 237/273 (86%), Gaps = 1/273 (0%) Query: 1 MSTPRIAFIGAGNMAASLIGGLRAQGVPAAQIRASDPGAEQRAKIAGEFAIDVVESNAEA 60 MS RIAFIGAGNMAASLIGGLRA+G+ AAQIRASDPGAE RA++ E I+ +NA+A Sbjct: 1 MSKTRIAFIGAGNMAASLIGGLRAKGLDAAQIRASDPGAETRARVTAEHGIETFANNADA 60 Query: 61 VADADVVVLSVKPQAMKAVCQALAPALKPEQLIVSIAAGIPCASLEAWLGQPRPVVRCMP 120 + ADVVVL+VKPQAMKAVC+AL P+L P QL+VSIAAGI CAS+ WLG +P+VRCMP Sbjct: 61 IQGADVVVLAVKPQAMKAVCEALRPSLAPNQLVVSIAAGITCASMNNWLGA-QPIVRCMP 119 Query: 121 NTPALLRQGASGLYANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGPAYF 180 NTPALLRQG SGLYA AQV+A Q +QA +LLSAVGIALWL++E Q+DAVTAVSGSGPAYF Sbjct: 120 NTPALLRQGVSGLYATAQVTAEQRQQAQELLSAVGIALWLNEEQQLDAVTAVSGSGPAYF 179 Query: 181 FLLMQAMTDAGEKLGLSRETASRLTLQTALGAAQMALSSEVEPAELRRRVTSPNGTTEAA 240 FLL++AMT AGEKLGL R+ A++LTLQTALGAA MA++S+V+ AELRRRVTSP GTTEAA Sbjct: 180 FLLIEAMTAAGEKLGLPRDIAAQLTLQTALGAAHMAVASDVDAAELRRRVTSPAGTTEAA 239 Query: 241 IKSFQANGFEALVEQALNAASQRSAELAEQLGQ 273 IK+FQA GFEALVE+AL AA+ RSAE+AEQLG+ Sbjct: 240 IKTFQAGGFEALVEKALGAAAHRSAEMAEQLGR 272 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: 281 Number of extensions: 5 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: 272 Length adjustment: 25 Effective length of query: 248 Effective length of database: 247 Effective search space: 61256 Effective search space used: 61256 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 AO353_08165 AO353_08165 (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.25414.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.9e-81 257.2 10.2 1.1e-80 257.0 10.2 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_08165 AO353_08165 pyrroline-5-carboxyl Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_08165 AO353_08165 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 257.0 10.2 1.1e-80 1.1e-80 1 263 [] 6 266 .. 6 266 .. 0.98 Alignments for each domain: == domain 1 score: 257.0 bits; conditional E-value: 1.1e-80 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvll 65 ia+iGaGnm+++l+ gl +kg +++i ++ +e +a+ +e g+e+ ++++ a++ advv+l lcl|FitnessBrowser__pseudo3_N2E3:AO353_08165 6 IAFIGAGNMAASLIGGLRAKGLD-AAQIRASDPGAETRARVTAEHGIETFANNADAIQGADVVVL 69 89**************9999765.8**************************************** PP TIGR00112 66 avKPqdleevlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtai 130 avKPq +++v++ l+ + + ++l++Si+AG+t++ ++++l+a +++vR+mPNt+a +++gv+++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_08165 70 AVKPQAMKAVCEALRP-SLAPNQLVVSIAAGITCASMNNWLGA-QPIVRCMPNTPALLRQGVSGL 132 **************99.7779********************86.99******************* PP TIGR00112 131 aassevseeqkelveellkavGkvveve.eklldavtalsGSgPAfvflliealadagvklGLpr 194 +a+++v++eq+++++ell+avG +++++ e++ldavta+sGSgPA++flliea+ +ag klGLpr lcl|FitnessBrowser__pseudo3_N2E3:AO353_08165 133 YATAQVTAEQRQQAQELLSAVGIALWLNeEQQLDAVTAVSGSGPAYFFLLIEAMTAAGEKLGLPR 197 ****************************99*********************************** PP TIGR00112 195 eeakelaaqtlkGaaklleesgehpalLkdkVtsPgGtTiaglavLeekgvrsavieaveaavkr 259 + a +l+ qt Gaa++ s+ ++a+L+ +VtsP+GtT a++++++++g+++ v++a+ aa++r lcl|FitnessBrowser__pseudo3_N2E3:AO353_08165 198 DIAAQLTLQTALGAAHMAVASDVDAAELRRRVTSPAGTTEAAIKTFQAGGFEALVEKALGAAAHR 262 ***************************************************************** PP TIGR00112 260 seeL 263 s e+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_08165 263 SAEM 266 9885 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (272 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 8.95 // [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