Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate WP_028310489.1 H566_RS0104400 pyrroline-5-carboxylate reductase
Query= SwissProt::P22008 (273 letters) >NCBI__GCF_000482785.1:WP_028310489.1 Length = 274 Score = 207 bits (528), Expect = 2e-58 Identities = 122/269 (45%), Positives = 167/269 (62%), Gaps = 4/269 (1%) Query: 6 IAFIGAGNMAASLIGGLRAQGVPAAQIRASDPGAEQRAKIAGEFAIDVVESNAEAVADAD 65 I FIG GNMA +LIGGL A+G +R +P RA + F +D A A+A A Sbjct: 8 ITFIGGGNMAQALIGGLIARGAVPRSLRVVEPNEATRALLIERFGVDARADAAGALAGAA 67 Query: 66 VVVLSVKPQAMKAVCQALAPALKPEQLIVSIAAGIPCASLEAWLGQPRPVVRCMPNTPAL 125 VVLSVKPQ ++ V LA + + L++SIAAGI + W+G R VVR MPNTPAL Sbjct: 68 AVVLSVKPQVLREVALGLAAEVG-DALVISIAAGIRARDIARWIGSDR-VVRTMPNTPAL 125 Query: 126 LRQGASGLYANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGPAYFFLLMQ 185 + +G +GL A + A A +LL AVG +W+DDE+++DAVTA+SGSGPAY FL ++ Sbjct: 126 IGEGITGLAALPACTTADQGLADELLGAVGRTVWVDDESKLDAVTAISGSGPAYVFLFIE 185 Query: 186 AMTDAGEKLGLSRETASRLTLQTALGAAQMALSSEVEPAELRRRVTSPNGTTEAAIKSFQ 245 A+ AG ++GL A L +QT G AQ+A S+ PA LR +VTS GTT AA+ + + Sbjct: 186 ALEAAGVRMGLGATEARALAIQTFAGGAQLAARSDDSPAVLREKVTSKGGTTFAALTTMR 245 Query: 246 ANGF-EALVEQALNAASQRSAELAEQLGQ 273 E+++ AL AA+ RSAEL ++ G+ Sbjct: 246 DKAVPESIIAGAL-AAAARSAELGDEFGR 273 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: 14 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: 273 Length of database: 274 Length adjustment: 25 Effective length of query: 248 Effective length of database: 249 Effective search space: 61752 Effective search space used: 61752 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 WP_028310489.1 H566_RS0104400 (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.31286.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.2e-79 250.9 6.4 9.2e-79 250.7 6.4 1.0 1 lcl|NCBI__GCF_000482785.1:WP_028310489.1 H566_RS0104400 pyrroline-5-carbo Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000482785.1:WP_028310489.1 H566_RS0104400 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 250.7 6.4 9.2e-79 9.2e-79 1 263 [] 8 267 .. 8 267 .. 0.97 Alignments for each domain: == domain 1 score: 250.7 bits; conditional E-value: 9.2e-79 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKP 69 i++iG+Gnm++al+ gl+++ga + ++ v+e++e+ +a l++++gv + +da+ a + a v+l+vKP lcl|NCBI__GCF_000482785.1:WP_028310489.1 8 ITFIGGGNMAQALIGGLIARGAV-PRSLRVVEPNEATRALLIERFGVDARADAAGALAGAAAVVLSVKP 75 79******************998.8******************************************** PP TIGR00112 70 qdleevlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevse 138 q+l+ev+ l+ + ++l+iSi+AG+++ ++ +++++ rvvR mPNt+a +g+g+t++aa +++ lcl|NCBI__GCF_000482785.1:WP_028310489.1 76 QVLREVALGLAA--EVGDALVISIAAGIRARDIARWIGS-DRVVRTMPNTPALIGEGITGLAALPACTT 141 *******88887..6689*******************86.88*************************** PP TIGR00112 139 eqkelveellkavGkvveve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlk 206 +++ l++ell avG +v+v+ e++ldavta+sGSgPA+vfl+ieal++agv++GL + ea++la qt++ lcl|NCBI__GCF_000482785.1:WP_028310489.1 142 ADQGLADELLGAVGRTVWVDdESKLDAVTAISGSGPAYVFLFIEALEAAGVRMGLGATEARALAIQTFA 210 ********************************************************************* PP TIGR00112 207 GaaklleesgehpalLkdkVtsPgGtTiaglavLeekgvrsavieaveaavkrseeL 263 G a+l ++s+++pa+L++kVts+gGtT a+l ++++k+v + +i++ aa++rs eL lcl|NCBI__GCF_000482785.1:WP_028310489.1 211 GGAQLAARSDDSPAVLREKVTSKGGTTFAALTTMRDKAVPESIIAGALAAAARSAEL 267 *********************************************999999999887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (274 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: 11.00 // [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