Align Carbamate kinase; EC 2.7.2.2 (characterized, see rationale)
to candidate PfGW456L13_1872 Carbamate kinase (EC 2.7.2.2)
Query= uniprot:P13982 (310 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1872 Length = 309 Score = 511 bits (1317), Expect = e-150 Identities = 253/310 (81%), Positives = 283/310 (91%), Gaps = 1/310 (0%) Query: 1 MRIVVALGGNALLRRGEPMTADNQRENVRIAAEQIAKVAPGNELVIAHGNGPQVGLLALQ 60 MRIVVALGGNALLRRGEPMTADNQR N+RIA EQIAK+ PGN+LVIAHGNGPQVGLL+LQ Sbjct: 1 MRIVVALGGNALLRRGEPMTADNQRANIRIATEQIAKIHPGNQLVIAHGNGPQVGLLSLQ 60 Query: 61 GAAYDKVSPYPLDVLGAETEGMIGYMIEQEMGNLLPFEVPFATILTQVEVDGKDPAFQNP 120 AAY VSPYPLDVLGAETEGMIGY+IEQE+GNLL FEVPFAT+LTQVEVD DPAF+NP Sbjct: 61 AAAYTSVSPYPLDVLGAETEGMIGYIIEQELGNLLDFEVPFATLLTQVEVDANDPAFKNP 120 Query: 121 TKPIGPVYSREEAERLAAEKGWSIAPDGDKFRRVVPSPRPKRIFEIRPVKWLLEKGTIVI 180 TKPIGPVY++EEAE LAAEKGW+IAPDGDK+RRVV SP+PKRIFEIRP+KWLLEK +IVI Sbjct: 121 TKPIGPVYTKEEAEALAAEKGWAIAPDGDKYRRVVASPKPKRIFEIRPIKWLLEKSSIVI 180 Query: 181 CAGGGGIPTMYDEAGKKLSGVEAVIDKDLCSSLLAQELVADILIIATDVDAAYVDWGKPT 240 CAGGGGIPTMY G KL GVEAVIDKDLCS+LLA++L AD+L+IATDV+AA++D+GKPT Sbjct: 181 CAGGGGIPTMYTSPG-KLEGVEAVIDKDLCSALLAEQLEADLLVIATDVNAAFIDFGKPT 239 Query: 241 QKAIAQAHPDELERLGFAAGSMGPKVQAAIEFARATGKDAVIGSLADIVAITEGKAGTRV 300 QKAIAQAHPDE+E+LGFAAGSMGPKVQAA EFAR TGK AVIGSL+DI AI +GKAGTR+ Sbjct: 240 QKAIAQAHPDEMEKLGFAAGSMGPKVQAACEFARHTGKVAVIGSLSDIEAIVQGKAGTRI 299 Query: 301 STRKAGIEYR 310 ST GI Y+ Sbjct: 300 STATPGISYQ 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: 399 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 PfGW456L13_1872 (Carbamate kinase (EC 2.7.2.2))
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.7778.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-133 430.6 0.2 1.6e-133 430.5 0.2 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1872 Carbamate kinase (EC 2.7.2.2) Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1872 Carbamate kinase (EC 2.7.2.2) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 430.5 0.2 1.6e-133 1.6e-133 1 308 [. 1 300 [. 1 301 [. 0.98 Alignments for each domain: == domain 1 score: 430.5 bits; conditional E-value: 1.6e-133 TIGR00746 1 kkvvvaLGGnallqrgekasaeeqrknvekaakqlvklakrgyelvithGngPqv 55 +++vvaLGGnall+rge ++a++qr n+++a++q++k++ g++lvi+hGngPqv lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1872 1 MRIVVALGGNALLRRGEPMTADNQRANIRIATEQIAKIHP-GNQLVIAHGNGPQV 54 589*************************************.************** PP TIGR00746 56 GalllqneaadsvpakPldvlgaesqgliGYllqqalkeelakeglekkvatvlt 110 G l lq +a+ sv+++Pldvlgae++g+iGY+++q+l + l +e ++at+lt lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1872 55 GLLSLQAAAYTSVSPYPLDVLGAETEGMIGYIIEQELGNLLD---FEVPFATLLT 106 *****************************************9...********** PP TIGR00746 111 qvivdekDeaFqnPtkpigpfydeeeakrlaaekgailkedagrgwRrvvpsPkP 165 qv+vd++D+aF+nPtkpigp+y++eea++laaekg+ ++ +g+++Rrvv+sPkP lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1872 107 QVEVDANDPAFKNPTKPIGPVYTKEEAEALAAEKGWAIAP-DGDKYRRVVASPKP 160 ****************************************.99************ PP TIGR00746 166 keiveaeviktLvekgvivissgGGGvPvvkdg.kelkGveaviDkDlasekLae 219 k+i+e++ ik+L+ek ivi++gGGG+P+++ +l+GveaviDkDl+s++Lae lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1872 161 KRIFEIRPIKWLLEKSSIVICAGGGGIPTMYTSpGKLEGVEAVIDKDLCSALLAE 215 *****************************9876256******************* PP TIGR00746 220 evnaDilviltdvdavyvnygkpdekkleevkveeleelakdgefaaGsmgPkve 274 +++aD lvi+tdv+a+++++gkp++k++++++++e+e+l faaGsmgPkv+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1872 216 QLEADLLVIATDVNAAFIDFGKPTQKAIAQAHPDEMEKLG----FAAGSMGPKVQ 266 ****************************************....*********** PP TIGR00746 275 aaiefvesrgkkaiitslekivealegkaGtvvv 308 aa ef++ +gk a+i+sl++i+++++gkaGt+++ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1872 267 AACEFARHTGKVAVIGSLSDIEAIVQGKAGTRIS 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: 11.27 // [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