Align Carbamate kinase; EC 2.7.2.2 (characterized, see rationale)
to candidate WP_090443604.1 BLS63_RS10655 carbamate kinase
Query= uniprot:P13982 (310 letters) >NCBI__GCF_900100495.1:WP_090443604.1 Length = 309 Score = 478 bits (1229), Expect = e-139 Identities = 238/310 (76%), Positives = 271/310 (87%), Gaps = 1/310 (0%) Query: 1 MRIVVALGGNALLRRGEPMTADNQRENVRIAAEQIAKVAPGNELVIAHGNGPQVGLLALQ 60 MRIVVALGGNALLRRGEP++A+NQR NVRIA QIA +A N+LVIAHGNGPQVGLLALQ Sbjct: 1 MRIVVALGGNALLRRGEPLSAENQRANVRIACAQIAGIAADNQLVIAHGNGPQVGLLALQ 60 Query: 61 GAAYDKVSPYPLDVLGAETEGMIGYMIEQEMGNLLPFEVPFATILTQVEVDGKDPAFQNP 120 GAAY V YPLDVLGAETEGMIGYMIEQE+GNLLPFEVPFAT+LTQVEVD DPAFQ+P Sbjct: 61 GAAYGAVGSYPLDVLGAETEGMIGYMIEQELGNLLPFEVPFATLLTQVEVDPADPAFQHP 120 Query: 121 TKPIGPVYSREEAERLAAEKGWSIAPDGDKFRRVVPSPRPKRIFEIRPVKWLLEKGTIVI 180 +KPIGPVYSR EAERLA E+GWSIA DG+ FRRVV SPRPKRIFEIRP++WLLE GT+VI Sbjct: 121 SKPIGPVYSRAEAERLARERGWSIAADGELFRRVVASPRPKRIFEIRPIQWLLEHGTVVI 180 Query: 181 CAGGGGIPTMYDEAGKKLSGVEAVIDKDLCSSLLAQELVADILIIATDVDAAYVDWGKPT 240 CAGGGGIPT+YDE ++L G+EAVIDKDLC++LLA++L A++L+IATDV A Y+DWG PT Sbjct: 181 CAGGGGIPTVYDEK-RQLKGIEAVIDKDLCAALLAEQLAAELLLIATDVPAVYLDWGLPT 239 Query: 241 QKAIAQAHPDELERLGFAAGSMGPKVQAAIEFARATGKDAVIGSLADIVAITEGKAGTRV 300 QK IA+AHPD LE+L FAAGSMGPKVQAA FAR TGK AVIG+L I I +G AGTR+ Sbjct: 240 QKVIARAHPDALEQLAFAAGSMGPKVQAACAFARHTGKPAVIGALDAIQGIVQGTAGTRI 299 Query: 301 STRKAGIEYR 310 S+ +AGIEYR Sbjct: 300 SSAQAGIEYR 309 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: 371 Number of extensions: 8 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 WP_090443604.1 BLS63_RS10655 (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.25056.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-125 403.3 0.0 3.5e-125 403.1 0.0 1.0 1 lcl|NCBI__GCF_900100495.1:WP_090443604.1 BLS63_RS10655 carbamate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900100495.1:WP_090443604.1 BLS63_RS10655 carbamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 403.1 0.0 3.5e-125 3.5e-125 1 308 [. 1 300 [. 1 301 [. 0.99 Alignments for each domain: == domain 1 score: 403.1 bits; conditional E-value: 3.5e-125 TIGR00746 1 kkvvvaLGGnallqrgekasaeeqrknvekaakqlvklakrgyelvithGngPqvGalllqneaadsvp 69 +++vvaLGGnall+rge +sae+qr nv++a +q++ +a+ ++lvi+hGngPqvG l+lq +a+ +v lcl|NCBI__GCF_900100495.1:WP_090443604.1 1 MRIVVALGGNALLRRGEPLSAENQRANVRIACAQIAGIAA-DNQLVIAHGNGPQVGLLALQGAAYGAVG 68 589***********************************99.9*************************** PP TIGR00746 70 akPldvlgaesqgliGYllqqalkeelakeglekkvatvltqvivdekDeaFqnPtkpigpfydeeeak 138 ++Pldvlgae++g+iGY+++q+l + l+ +e ++at+ltqv+vd++D+aFq+P kpigp+y+++ea+ lcl|NCBI__GCF_900100495.1:WP_090443604.1 69 SYPLDVLGAETEGMIGYMIEQELGNLLP---FEVPFATLLTQVEVDPADPAFQHPSKPIGPVYSRAEAE 134 ****************************...************************************** PP TIGR00746 139 rlaaekgailkedagrgwRrvvpsPkPkeiveaeviktLvekgvivissgGGGvPvvkdgke.lkGvea 206 rla+e+g++++ +g+ +Rrvv+sP+Pk+i+e++ i++L+e+g++vi++gGGG+P+v+d+k+ lkG+ea lcl|NCBI__GCF_900100495.1:WP_090443604.1 135 RLARERGWSIAA-DGELFRRVVASPRPKRIFEIRPIQWLLEHGTVVICAGGGGIPTVYDEKRqLKGIEA 202 ***********9.9******************************************9998766****** PP TIGR00746 207 viDkDlasekLaeevnaDilviltdvdavyvnygkpdekkleevkveeleelakdgefaaGsmgPkvea 275 viDkDl++++Lae++ a+ l+i+tdv avy+++g p++k +++++++ le+la faaGsmgPkv+a lcl|NCBI__GCF_900100495.1:WP_090443604.1 203 VIDKDLCAALLAEQLAAELLLIATDVPAVYLDWGLPTQKVIARAHPDALEQLA----FAAGSMGPKVQA 267 *****************************************************....************ PP TIGR00746 276 aiefvesrgkkaiitslekivealegkaGtvvv 308 a f++ +gk a+i++l+ i+ +++g aGt+++ lcl|NCBI__GCF_900100495.1:WP_090443604.1 268 ACAFARHTGKPAVIGALDAIQGIVQGTAGTRIS 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: 00:00:00.01 # Mc/sec: 8.84 // [ok]
This GapMind analysis is from Sep 24 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