Align pyrroline-5-carboxylate reductase (EC 1.5.1.2) (characterized)
to candidate WP_085219465.1 B9N75_RS07535 pyrroline-5-carboxylate reductase
Query= reanno::Caulo:CCNA_00528 (260 letters) >NCBI__GCF_900177405.1:WP_085219465.1 Length = 269 Score = 177 bits (449), Expect = 2e-49 Identities = 105/260 (40%), Positives = 143/260 (55%), Gaps = 5/260 (1%) Query: 3 PILLLGAGRMGGALIQGWQAAGAFDAADLIIRDPHVDAAAFAGAVVNPPLETLGAAKTVL 62 P ++G G M GA+++GW AAG +IR A + P + A + Sbjct: 7 PFWMIGCGNMAGAMLEGWLAAGLDPDRVTVIRPSGTPAPGGVRTLTALPADETPAI--AM 64 Query: 63 LAVKPQIWREAIADVVPHLAPDAVIVSIAAGVRAADISQAFGG-RRVARVMPTTAVAIGQ 121 L VKPQ + + P LAP+ ++VSI AGV A + F R + R MP T VA+ + Sbjct: 65 LGVKPQKLDDVAPSLAPALAPETILVSILAGVETASLRARFAAPRTIVRAMPNTPVALRK 124 Query: 122 GAASLYADDAEALARAR--ALFAPLAAVAELASEDLMHAATAVSGSAPAYLYAFIEALEA 179 GA L++D A AR AL L + EDL+H A+ GS PA+++ FI+A+ A Sbjct: 125 GATGLFSDSAHPAAREAVGALMTALGHAEWVEDEDLLHVVGALCGSGPAFVFRFIDAIAA 184 Query: 180 AGAAQGLDPAQSARLARATIIGAAALMAQSGEEPAELRKQVTSPGGTTAAALSVLMGAGG 239 AGAA GL P Q+ARLA AT+ GA +L S E P EL +VTSPGG TA L +L Sbjct: 185 AGAALGLPPEQAARLALATVDGAGSLAGSSPETPHELAVRVTSPGGMTAKGLDILDDDAA 244 Query: 240 FGDLLPKALDAAVARSKELG 259 DL+ + L+AAV RS+E+G Sbjct: 245 LADLVRRTLEAAVDRSREMG 264 Lambda K H 0.318 0.131 0.366 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: 198 Number of extensions: 7 Number of successful extensions: 4 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: 260 Length of database: 269 Length adjustment: 25 Effective length of query: 235 Effective length of database: 244 Effective search space: 57340 Effective search space used: 57340 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 (21.7 bits) S2: 47 (22.7 bits)
Align candidate WP_085219465.1 B9N75_RS07535 (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.1964618.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-65 206.6 0.0 3.2e-65 206.4 0.0 1.1 1 NCBI__GCF_900177405.1:WP_085219465.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900177405.1:WP_085219465.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 206.4 0.0 3.2e-65 3.2e-65 3 263 .] 10 263 .. 8 263 .. 0.94 Alignments for each domain: == domain 1 score: 206.4 bits; conditional E-value: 3.2e-65 TIGR00112 3 iiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKPqdleev 75 +iG+Gnm+ a+l+g+l++g ++++ vi++s + + + +l + + + + +l+vKPq+l++v NCBI__GCF_900177405.1:WP_085219465.1 10 MIGCGNMAGAMLEGWLAAGLD-PDRVTVIRPSGTPAPGGVRTLTALPADE------TPAIAMLGVKPQKLDDV 75 79***************9775.9********9999888888875444443......445779*********** PP TIGR00112 76 laelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevseeqkelveell 148 + +l+ + e++l+SilAGv+++ l+ ++a +++vR+mPNt++++++g+t+++ + ++++ +e v +l+ NCBI__GCF_900177405.1:WP_085219465.1 76 APSLAP-ALAPETILVSILAGVETASLRARFAAPRTIVRAMPNTPVALRKGATGLFSD-SAHPAAREAVGALM 146 *****9.6669*********************************************99.588999******** PP TIGR00112 149 kavGkvveve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaaklleesgehpa 220 +a+G++ +ve e+ll+ v al+GSgPAfvf +i+a+a+ag +lGLp e+a +la +t+ Ga+ l s e+p NCBI__GCF_900177405.1:WP_085219465.1 147 TALGHAEWVEdEDLLHVVGALCGSGPAFVFRFIDAIAAAGAALGLPPEQAARLALATVDGAGSLAGSSPETPH 219 ************************************************************************* PP TIGR00112 221 lLkdkVtsPgGtTiaglavLeekg.vrsavieaveaavkrseeL 263 +L +VtsPgG T++gl +L +++ + + v +++eaav+rs+e+ NCBI__GCF_900177405.1:WP_085219465.1 220 ELAVRVTSPGGMTAKGLDILDDDAaLADLVRRTLEAAVDRSREM 263 ********************988769***************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (269 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: 17.13 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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