Align Carbamate kinase; EC 2.7.2.2 (characterized, see rationale)
to candidate BPHYT_RS27690 BPHYT_RS27690 carbamate kinase
Query= uniprot:P13982 (310 letters) >FitnessBrowser__BFirm:BPHYT_RS27690 Length = 302 Score = 358 bits (919), Expect = e-104 Identities = 181/301 (60%), Positives = 223/301 (74%), Gaps = 1/301 (0%) Query: 1 MRIVVALGGNALLRRGEPMTADNQRENVRIAAEQIAKVAPGNELVIAHGNGPQVGLLALQ 60 MRI++ALGGNALLRRGEPMT NQ N+R AA QI ++A GN+LV+AHGNGPQVGLLALQ Sbjct: 1 MRILIALGGNALLRRGEPMTMANQIANIRRAASQIGQLADGNQLVVAHGNGPQVGLLALQ 60 Query: 61 GAAYDKV-SPYPLDVLGAETEGMIGYMIEQEMGNLLPFEVPFATILTQVEVDGKDPAFQN 119 AA + PLDVL AE+EGMIGY++EQE+ N+LP + AT+LT+VEVD DPAF++ Sbjct: 61 AAASGPAGAASPLDVLDAESEGMIGYLLEQELANVLPVQRQVATLLTRVEVDADDPAFEH 120 Query: 120 PTKPIGPVYSREEAERLAAEKGWSIAPDGDKFRRVVPSPRPKRIFEIRPVKWLLEKGTIV 179 PTKPIGPVY++ +A+ LA GW+IA DG FRRVV SPRP+RI +RP++WLL+ +V Sbjct: 121 PTKPIGPVYTKAQAQDLARRNGWTIAEDGAGFRRVVASPRPRRIVALRPIEWLLDHDVVV 180 Query: 180 ICAGGGGIPTMYDEAGKKLSGVEAVIDKDLCSSLLAQELVADILIIATDVDAAYVDWGKP 239 + AGGGGIP G+ GVEAVIDKD CS+LLA EL AD+L+IATDVDA Y DW P Sbjct: 181 VAAGGGGIPVKVAPDGQTRVGVEAVIDKDRCSALLAAELAADLLLIATDVDAVYADWRTP 240 Query: 240 TQKAIAQAHPDELERLGFAAGSMGPKVQAAIEFARATGKDAVIGSLADIVAITEGKAGTR 299 ++ + EL + FAAGSM PKV+AA +F TGK AVIGSL I A+ G AGTR Sbjct: 241 RERVLHDVPVAELRSMSFAAGSMAPKVEAACDFVAHTGKPAVIGSLEHIAAMANGTAGTR 300 Query: 300 V 300 + Sbjct: 301 I 301 Lambda K H 0.317 0.136 0.393 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: 336 Number of extensions: 18 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: 310 Length of database: 302 Length adjustment: 27 Effective length of query: 283 Effective length of database: 275 Effective search space: 77825 Effective search space used: 77825 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: 48 (23.1 bits)
Align candidate BPHYT_RS27690 BPHYT_RS27690 (carbamate kinase)
to HMM TIGR00746 (arcC: carbamate kinase (EC 2.7.2.2))
# 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/TIGR00746.hmm # target sequence database: /tmp/gapView.28176.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00746 [M=309] Accession: TIGR00746 Description: arcC: carbamate kinase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.9e-120 386.5 0.2 4.3e-120 386.4 0.2 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS27690 BPHYT_RS27690 carbamate kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS27690 BPHYT_RS27690 carbamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 386.4 0.2 4.3e-120 4.3e-120 2 308 .. 2 302 .] 1 302 [] 0.98 Alignments for each domain: == domain 1 score: 386.4 bits; conditional E-value: 4.3e-120 TIGR00746 2 kvvvaLGGnallqrgekasaeeqrknvekaakqlvklakrgyelvithGngPqvGalllqneaads.vpa 70 ++ +aLGGnall+rge +++ +q+ n+++aa+q+ +la g++lv++hGngPqvG l+lq +a+ +a lcl|FitnessBrowser__BFirm:BPHYT_RS27690 2 RILIALGGNALLRRGEPMTMANQIANIRRAASQIGQLAD-GNQLVVAHGNGPQVGLLALQAAASGPaGAA 70 899***********************************9.*********************999886899 PP TIGR00746 71 kPldvlgaesqgliGYllqqalkeelakeglekkvatvltqvivdekDeaFqnPtkpigpfydeeeakrl 140 Pldvl aes+g+iGYll+q+l ++l+ ++++vat+lt+v+vd++D+aF++Ptkpigp+y++++a+ l lcl|FitnessBrowser__BFirm:BPHYT_RS27690 71 SPLDVLDAESEGMIGYLLEQELANVLP---VQRQVATLLTRVEVDADDPAFEHPTKPIGPVYTKAQAQDL 137 ***************************...9*************************************** PP TIGR00746 141 aaekgailkedagrgwRrvvpsPkPkeiveaeviktLvekgvivissgGGGvPvv..kdgkelkGveavi 208 a+ +g++++e +g+g+Rrvv+sP+P++iv + i++L++++v+v+++gGGG+Pv+ dg++ Gveavi lcl|FitnessBrowser__BFirm:BPHYT_RS27690 138 ARRNGWTIAE-DGAGFRRVVASPRPRRIVALRPIEWLLDHDVVVVAAGGGGIPVKvaPDGQTRVGVEAVI 206 **********.9*****************************************86226899999****** PP TIGR00746 209 DkDlasekLaeevnaDilviltdvdavyvnygkpdekkleevkveeleelakdgefaaGsmgPkveaaie 278 DkD++s++La e+ aD l+i+tdvdavy ++ +p e+ l++v v+el+++ faaGsm+Pkveaa + lcl|FitnessBrowser__BFirm:BPHYT_RS27690 207 DKDRCSALLAAELAADLLLIATDVDAVYADWRTPRERVLHDVPVAELRSMS----FAAGSMAPKVEAACD 272 ***************************************************....*************** PP TIGR00746 279 fvesrgkkaiitslekivealegkaGtvvv 308 fv +gk a+i+sle+i ++ +g aGt+++ lcl|FitnessBrowser__BFirm:BPHYT_RS27690 273 FVAHTGKPAVIGSLEHIAAMANGTAGTRII 302 ***************************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (302 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: 00:00:00.01 # Mc/sec: 9.12 // [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