Align Carbamate kinase; EC 2.7.2.2 (characterized, see rationale)
to candidate GFF4363 PS417_22340 carbamate kinase
Query= uniprot:P13982 (310 letters) >FitnessBrowser__WCS417:GFF4363 Length = 309 Score = 514 bits (1323), Expect = e-150 Identities = 255/309 (82%), Positives = 282/309 (91%), Gaps = 1/309 (0%) Query: 1 MRIVVALGGNALLRRGEPMTADNQRENVRIAAEQIAKVAPGNELVIAHGNGPQVGLLALQ 60 MRIVVALGGNALLRRGEPMTADNQR N+RIA EQIAK+ GNELVIAHGNGPQVGLL+LQ Sbjct: 1 MRIVVALGGNALLRRGEPMTADNQRANIRIATEQIAKIHAGNELVIAHGNGPQVGLLSLQ 60 Query: 61 GAAYDKVSPYPLDVLGAETEGMIGYMIEQEMGNLLPFEVPFATILTQVEVDGKDPAFQNP 120 AAY +VSPYPLDVLGAETEGMIGY+IEQE+GNLL FEVPFAT+LTQVEVD KDPAFQNP Sbjct: 61 AAAYTQVSPYPLDVLGAETEGMIGYIIEQELGNLLDFEVPFATLLTQVEVDAKDPAFQNP 120 Query: 121 TKPIGPVYSREEAERLAAEKGWSIAPDGDKFRRVVPSPRPKRIFEIRPVKWLLEKGTIVI 180 TKPIGPVYS+ EAE+LAAEKGW+IAPDGDK+RRVV SPRPKRIFEIRP+ WLL+KG+IVI Sbjct: 121 TKPIGPVYSKAEAEKLAAEKGWAIAPDGDKYRRVVASPRPKRIFEIRPITWLLDKGSIVI 180 Query: 181 CAGGGGIPTMYDEAGKKLSGVEAVIDKDLCSSLLAQELVADILIIATDVDAAYVDWGKPT 240 CAGGGGIPTMY E G KL G+EAVIDKDLCSSLLA +L AD+L+IATDV+AA++D+GKPT Sbjct: 181 CAGGGGIPTMYGEDG-KLRGIEAVIDKDLCSSLLASQLKADLLVIATDVNAAFIDFGKPT 239 Query: 241 QKAIAQAHPDELERLGFAAGSMGPKVQAAIEFARATGKDAVIGSLADIVAITEGKAGTRV 300 QKAI QAHPDE+E+LGFAAGSMGPKVQAA EFAR TGK AVIGSL+DI AI +G AGTR+ Sbjct: 240 QKAIGQAHPDEMEKLGFAAGSMGPKVQAACEFARQTGKTAVIGSLSDIEAIVQGSAGTRI 299 Query: 301 STRKAGIEY 309 ST K GI Y Sbjct: 300 STAKPGITY 308 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: 395 Number of extensions: 14 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: 309 Length adjustment: 27 Effective length of query: 283 Effective length of database: 282 Effective search space: 79806 Effective search space used: 79806 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 GFF4363 PS417_22340 (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.32224.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-133 429.5 0.1 3.6e-133 429.3 0.1 1.0 1 lcl|FitnessBrowser__WCS417:GFF4363 PS417_22340 carbamate kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__WCS417:GFF4363 PS417_22340 carbamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 429.3 0.1 3.6e-133 3.6e-133 1 308 [. 1 300 [. 1 301 [. 0.98 Alignments for each domain: == domain 1 score: 429.3 bits; conditional E-value: 3.6e-133 TIGR00746 1 kkvvvaLGGnallqrgekasaeeqrknvekaakqlvklakrgyelvithGngPqvGalllqneaadsvpakPldv 75 +++vvaLGGnall+rge ++a++qr n+++a++q++k+++ g+elvi+hGngPqvG l lq +a+ +v+++Pldv lcl|FitnessBrowser__WCS417:GFF4363 1 MRIVVALGGNALLRRGEPMTADNQRANIRIATEQIAKIHA-GNELVIAHGNGPQVGLLSLQAAAYTQVSPYPLDV 74 589************************************9.********************************** PP TIGR00746 76 lgaesqgliGYllqqalkeelakeglekkvatvltqvivdekDeaFqnPtkpigpfydeeeakrlaaekgailke 150 lgae++g+iGY+++q+l + l +e ++at+ltqv+vd+kD+aFqnPtkpigp+y+++ea++laaekg+ ++ lcl|FitnessBrowser__WCS417:GFF4363 75 LGAETEGMIGYIIEQELGNLLD---FEVPFATLLTQVEVDAKDPAFQNPTKPIGPVYSKAEAEKLAAEKGWAIAP 146 *********************9...************************************************** PP TIGR00746 151 dagrgwRrvvpsPkPkeiveaeviktLvekgvivissgGGGvPvvk.dgkelkGveaviDkDlasekLaeevnaD 224 +g+++Rrvv+sP+Pk+i+e++ i +L++kg ivi++gGGG+P+++ ++ +l+G+eaviDkDl+s++La +++aD lcl|FitnessBrowser__WCS417:GFF4363 147 -DGDKYRRVVASPRPKRIFEIRPITWLLDKGSIVICAGGGGIPTMYgEDGKLRGIEAVIDKDLCSSLLASQLKAD 220 .99*****************************************9835567************************ PP TIGR00746 225 ilviltdvdavyvnygkpdekkleevkveeleelakdgefaaGsmgPkveaaiefvesrgkkaiitslekiveal 299 lvi+tdv+a+++++gkp++k++ +++++e+e+l faaGsmgPkv+aa ef++++gk+a+i+sl++i++++ lcl|FitnessBrowser__WCS417:GFF4363 221 LLVIATDVNAAFIDFGKPTQKAIGQAHPDEMEKLG----FAAGSMGPKVQAACEFARQTGKTAVIGSLSDIEAIV 291 ***********************************....************************************ PP TIGR00746 300 egkaGtvvv 308 +g aGt+++ lcl|FitnessBrowser__WCS417:GFF4363 292 QGSAGTRIS 300 *******97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (309 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: 11.34 // [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