Align Carbamate kinase; EC 2.7.2.2 (characterized, see rationale)
to candidate AZOBR_RS13245 AZOBR_RS13245 carbamate kinase
Query= uniprot:P13982 (310 letters) >FitnessBrowser__azobra:AZOBR_RS13245 Length = 317 Score = 418 bits (1074), Expect = e-121 Identities = 214/306 (69%), Positives = 246/306 (80%), Gaps = 6/306 (1%) Query: 1 MRIVVALGGNALLRRGEPMTADNQRENVRIAAEQIAKVAPGNELVIAHGNGPQVGLLALQ 60 MR+VVALGGNALL+RGEPMTAD QR N+RIAAE +A VA ++LVI+HGNGPQVGLLALQ Sbjct: 1 MRVVVALGGNALLKRGEPMTADVQRRNIRIAAEAMAPVAREHQLVISHGNGPQVGLLALQ 60 Query: 61 GAAYDKVSPYPLDVLGAETEGMIGYMIEQEMGNLLPFEVPFATILTQVEVDGKDPAFQNP 120 GAAY YPLDVLGAETEGMIGYMIEQE+GNLLPFEVPFAT+LT VEVDG DPAF +P Sbjct: 61 GAAYRPDEAYPLDVLGAETEGMIGYMIEQELGNLLPFEVPFATLLTMVEVDGDDPAFGDP 120 Query: 121 TKPIGPVYSREEAERLAAEKGWSIAPDGDKFRRVVPSPRPKRIFEIRPVKWLLEKGTIVI 180 TK +GPVY EA+R+AAEKGW DG +RRVVPSP PKRIFEIRP++WLL++GTIVI Sbjct: 121 TKFVGPVYGAAEAQRIAAEKGWVFKADGASWRRVVPSPAPKRIFEIRPIRWLLDQGTIVI 180 Query: 181 CAGGGGIPTMYDEA----GKK--LSGVEAVIDKDLCSSLLAQELVADILIIATDVDAAYV 234 CAGGGGIPTMY A GK+ L GVEAVIDKDLCS LLA+EL AD+LI+ATD +A ++ Sbjct: 181 CAGGGGIPTMYQPAMHQPGKERTLVGVEAVIDKDLCSELLARELGADLLIMATDAEAVFL 240 Query: 235 DWGKPTQKAIAQAHPDELERLGFAAGSMGPKVQAAIEFARATGKDAVIGSLADIVAITEG 294 WG P +AI +A PD + R F AGSMGPKV AA FA ATG+ A IG+LADI AI G Sbjct: 241 GWGTPDARAIHRASPDAMGRYSFPAGSMGPKVDAACRFATATGRTAAIGALADIPAIVRG 300 Query: 295 KAGTRV 300 + GT + Sbjct: 301 EKGTLI 306 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: 372 Number of extensions: 12 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: 317 Length adjustment: 27 Effective length of query: 283 Effective length of database: 290 Effective search space: 82070 Effective search space used: 82070 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 AZOBR_RS13245 AZOBR_RS13245 (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.10206.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-116 375.3 0.0 1.2e-116 375.1 0.0 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS13245 AZOBR_RS13245 carbamate kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS13245 AZOBR_RS13245 carbamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 375.1 0.0 1.2e-116 1.2e-116 1 307 [. 1 306 [. 1 308 [. 0.96 Alignments for each domain: == domain 1 score: 375.1 bits; conditional E-value: 1.2e-116 TIGR00746 1 kkvvvaLGGnallqrgekasaeeqrknvekaakqlvklakrgyelvithGngPqvGalllqneaadsvp 69 ++vvvaLGGnall+rge ++a+ qr+n+++aa++++ +a+ ++lvi+hGngPqvG l+lq +a+ + lcl|FitnessBrowser__azobra:AZOBR_RS13245 1 MRVVVALGGNALLKRGEPMTADVQRRNIRIAAEAMAPVAR-EHQLVISHGNGPQVGLLALQGAAYRPDE 68 589***********************************99.9*************************** PP TIGR00746 70 akPldvlgaesqgliGYllqqalkeelakeglekkvatvltqvivdekDeaFqnPtkpigpfydeeeak 138 a+Pldvlgae++g+iGY+++q+l + l+ +e ++at+lt v+vd +D+aF +Ptk++gp+y +ea+ lcl|FitnessBrowser__azobra:AZOBR_RS13245 69 AYPLDVLGAETEGMIGYMIEQELGNLLP---FEVPFATLLTMVEVDGDDPAFGDPTKFVGPVYGAAEAQ 134 ****************************...************************************** PP TIGR00746 139 rlaaekgailkedagrgwRrvvpsPkPkeiveaeviktLvekgvivissgGGGvPvvkdgke....... 200 r aaekg+ +k +g+ wRrvvpsP Pk+i+e++ i++L+++g+ivi++gGGG+P++++ + lcl|FitnessBrowser__azobra:AZOBR_RS13245 135 RIAAEKGWVFKA-DGASWRRVVPSPAPKRIFEIRPIRWLLDQGTIVICAGGGGIPTMYQPAMhqpgker 202 ***********9.9******************************************9863322223335 PP TIGR00746 201 .lkGveaviDkDlasekLaeevnaDilviltdvdavyvnygkpdekkleevkveeleelakdgefaaGs 268 l GveaviDkDl+se+La+e++aD l+++td++av++ +g+pd +++++++++ + ++ f aGs lcl|FitnessBrowser__azobra:AZOBR_RS13245 203 tLVGVEAVIDKDLCSELLARELGADLLIMATDAEAVFLGWGTPDARAIHRASPDAMGRYS----FPAGS 267 5***********************************************************....***** PP TIGR00746 269 mgPkveaaiefvesrgkkaiitslekivealegkaGtvv 307 mgPkv aa +f+ ++g +a i++l++i +++ g+ Gt + lcl|FitnessBrowser__azobra:AZOBR_RS13245 268 MGPKVDAACRFATATGRTAAIGALADIPAIVRGEKGTLI 306 *************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (317 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: 11.84 // [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