Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate WP_012475720.1 CPHAMN1_RS11680 pyrroline-5-carboxylate reductase
Query= SwissProt::Q9HH99 (270 letters) >NCBI__GCF_000020545.1:WP_012475720.1 Length = 266 Score = 178 bits (452), Expect = 9e-50 Identities = 103/269 (38%), Positives = 153/269 (56%), Gaps = 3/269 (1%) Query: 1 MENQKIGFIGAGKMGSALMQGTIKAGIVTPENIGASDVYEPFLKDLQAKLGIRVSTDNAV 60 M IGFIG G++ AL+ G + I D + ++ + GIR V Sbjct: 1 MNRTTIGFIGTGRIARALISGLAQDDSF---EISGFDKNPEAAEGVKREYGIRACPTLQV 57 Query: 61 IVRESDILILAVKPQTLSSVLSNLKNEITSEKLVISIAAGVPLSTYEDALLEGTRVVRVM 120 + +D ++LAVKP + VL+ L+ +++ L+IS+AAG+ + RV+RVM Sbjct: 58 LAESADSIVLAVKPYQIEEVLTELRGHLSAAHLLISVAAGITSGFIREHSRNDMRVIRVM 117 Query: 121 PNIAATVSEAASGIAPGKNATPEDLKAALEIFSAVGTAVQVPESLMDAVTGLSGSGPAFI 180 PN A E + ++ G AT D+ A +IFSA+G + + ESLMDA T +SGSGPA++ Sbjct: 118 PNTPAFAGEGMTAVSAGALATSADIATAEKIFSAIGRVLVLDESLMDAATAVSGSGPAYM 177 Query: 181 FPVIEAMADGAVLEGMDRKSALTLAAQTVLGAAKMALETGMHPGELKDMVTSPAGTTIQG 240 F +I ++A+G L G+ K AL L AQT+LGAA+MAL++ P EL VT+P GTT G Sbjct: 178 FHIISSIAEGGKLCGLSEKEALILTAQTMLGAARMALDSQKSPEELIKEVTTPGGTTEAG 237 Query: 241 IHSLEEAGIRAAFMNAVIRASERSKELGK 269 + + +R A ++ V A+ERS EL K Sbjct: 238 LKQMISHDVRQAMIDTVKAATERSLELKK 266 Lambda K H 0.313 0.130 0.343 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: 173 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: 270 Length of database: 266 Length adjustment: 25 Effective length of query: 245 Effective length of database: 241 Effective search space: 59045 Effective search space used: 59045 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 47 (22.7 bits)
Align candidate WP_012475720.1 CPHAMN1_RS11680 (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.26425.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-80 256.6 4.8 1.6e-80 256.5 4.8 1.0 1 lcl|NCBI__GCF_000020545.1:WP_012475720.1 CPHAMN1_RS11680 pyrroline-5-carb Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020545.1:WP_012475720.1 CPHAMN1_RS11680 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 256.5 4.8 1.6e-80 1.6e-80 1 263 [] 6 264 .. 6 264 .. 0.98 Alignments for each domain: == domain 1 score: 256.5 bits; conditional E-value: 1.6e-80 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKP 69 i++iG G++++al+sgl + ++ ei ++++e+++ e+g++++ + + +++ ad ++lavKP lcl|NCBI__GCF_000020545.1:WP_012475720.1 6 IGFIGTGRIARALISGLAQD---DSFEISGFDKNPEAAEGVKREYGIRACPTLQVLAESADSIVLAVKP 71 89**************9997...56799999************************************** PP TIGR00112 70 qdleevlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevse 138 +++eevl+el++ + ++++lliS++AG+t ++++ ++ rv+RvmPNt+a g+g+ta++a++ +++ lcl|NCBI__GCF_000020545.1:WP_012475720.1 72 YQIEEVLTELRG-HLSAAHLLISVAAGITSGFIREHSRNDMRVIRVMPNTPAFAGEGMTAVSAGALATS 139 ************.77799*************************************************** PP TIGR00112 139 eqkelveellkavGkvveveeklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkG 207 ++ +++e++++a+G v+ ++e+l+da+ta+sGSgPA++f++i ++a++g +GL+++ea+ l+aqt+ G lcl|NCBI__GCF_000020545.1:WP_012475720.1 140 ADIATAEKIFSAIGRVLVLDESLMDAATAVSGSGPAYMFHIISSIAEGGKLCGLSEKEALILTAQTMLG 208 ********************************************************************* PP TIGR00112 208 aaklleesgehpalLkdkVtsPgGtTiaglavLeekgvrsavieaveaavkrseeL 263 aa++ s+++p++L+++Vt+PgGtT agl+ + ++vr+a+i++v+aa++rs eL lcl|NCBI__GCF_000020545.1:WP_012475720.1 209 AARMALDSQKSPEELIKEVTTPGGTTEAGLKQMISHDVRQAMIDTVKAATERSLEL 264 ****************************************************9887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (266 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 7.41 // [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