Align Carbamate kinase; EC 2.7.2.2 (characterized, see rationale)
to candidate GFF269 Psest_0270 carbamate kinase
Query= uniprot:P13982 (310 letters) >FitnessBrowser__psRCH2:GFF269 Length = 307 Score = 482 bits (1241), Expect = e-141 Identities = 237/307 (77%), Positives = 273/307 (88%), Gaps = 1/307 (0%) Query: 1 MRIVVALGGNALLRRGEPMTADNQRENVRIAAEQIAKVAPGNELVIAHGNGPQVGLLALQ 60 MRIV+ALGGNALLRRGEP++ADNQRENVR A QIA++A GNELV+AHGNGPQVGLLALQ Sbjct: 1 MRIVIALGGNALLRRGEPLSADNQRENVRTACMQIARIAAGNELVVAHGNGPQVGLLALQ 60 Query: 61 GAAYDKVSPYPLDVLGAETEGMIGYMIEQEMGNLLPFEVPFATILTQVEVDGKDPAFQNP 120 GAAY V YPLDVLGAETEGMIGY+IEQE+GNLLPFEVP AT+LTQVEVD +DPAF+ P Sbjct: 61 GAAYKDVPVYPLDVLGAETEGMIGYIIEQELGNLLPFEVPMATLLTQVEVDPEDPAFKQP 120 Query: 121 TKPIGPVYSREEAERLAAEKGWSIAPDGDKFRRVVPSPRPKRIFEIRPVKWLLEKGTIVI 180 +KPIGPVYSREEAERLA EKGW+IA DGD+FRRVVPSPRPKRIFEIRP+ WLL+KG++VI Sbjct: 121 SKPIGPVYSREEAERLAEEKGWAIAADGDRFRRVVPSPRPKRIFEIRPIGWLLDKGSVVI 180 Query: 181 CAGGGGIPTMYDEAGKKLSGVEAVIDKDLCSSLLAQELVADILIIATDVDAAYVDWGKPT 240 CAGGGGIPT+YD++G +L GVEAVIDKDLCS+LLA++L AD+L+IATDVD AY+DWG P Sbjct: 181 CAGGGGIPTVYDQSG-RLQGVEAVIDKDLCSALLAEQLKADLLVIATDVDGAYLDWGTPQ 239 Query: 241 QKAIAQAHPDELERLGFAAGSMGPKVQAAIEFARATGKDAVIGSLADIVAITEGKAGTRV 300 Q+ I++AHPD+L+ GFAAGSMGPKVQAA EFAR TG AVIGSL I AI +G+AGTRV Sbjct: 240 QRRISEAHPDQLQSRGFAAGSMGPKVQAACEFARNTGNVAVIGSLEQIEAIIKGQAGTRV 299 Query: 301 STRKAGI 307 S AG+ Sbjct: 300 SLEAAGL 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: 384 Number of extensions: 10 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: 307 Length adjustment: 27 Effective length of query: 283 Effective length of database: 280 Effective search space: 79240 Effective search space used: 79240 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 GFF269 Psest_0270 (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.3051.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-131 423.2 0.0 2.9e-131 423.0 0.0 1.0 1 lcl|FitnessBrowser__psRCH2:GFF269 Psest_0270 carbamate kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__psRCH2:GFF269 Psest_0270 carbamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 423.0 0.0 2.9e-131 2.9e-131 1 308 [. 1 300 [. 1 301 [. 0.99 Alignments for each domain: == domain 1 score: 423.0 bits; conditional E-value: 2.9e-131 TIGR00746 1 kkvvvaLGGnallqrgekasaeeqrknvekaakqlvklakrgyelvithGngPqvGalllqneaadsvpakPldvl 76 +++v+aLGGnall+rge +sa++qr+nv++a q++++a+ g+elv++hGngPqvG l+lq +a+++vp +Pldvl lcl|FitnessBrowser__psRCH2:GFF269 1 MRIVIALGGNALLRRGEPLSADNQRENVRTACMQIARIAA-GNELVVAHGNGPQVGLLALQGAAYKDVPVYPLDVL 75 589***********************************99.*********************************** PP TIGR00746 77 gaesqgliGYllqqalkeelakeglekkvatvltqvivdekDeaFqnPtkpigpfydeeeakrlaaekgailkeda 152 gae++g+iGY+++q+l + l+ +e ++at+ltqv+vd++D+aF++P kpigp+y++eea+rla ekg+ ++ + lcl|FitnessBrowser__psRCH2:GFF269 76 GAETEGMIGYIIEQELGNLLP---FEVPMATLLTQVEVDPEDPAFKQPSKPIGPVYSREEAERLAEEKGWAIAA-D 147 *********************...*************************************************9.9 PP TIGR00746 153 grgwRrvvpsPkPkeiveaeviktLvekgvivissgGGGvPvvkdgke.lkGveaviDkDlasekLaeevnaDilv 227 g+++RrvvpsP+Pk+i+e++ i +L++kg +vi++gGGG+P+v+d+++ l+GveaviDkDl+s++Lae+++aD lv lcl|FitnessBrowser__psRCH2:GFF269 148 GDRFRRVVPSPRPKRIFEIRPIGWLLDKGSVVICAGGGGIPTVYDQSGrLQGVEAVIDKDLCSALLAEQLKADLLV 223 9******************************************999877*************************** PP TIGR00746 228 iltdvdavyvnygkpdekkleevkveeleelakdgefaaGsmgPkveaaiefvesrgkkaiitslekivealegka 303 i+tdvd +y+++g+p++++++e++++ l++ faaGsmgPkv+aa ef++++g+ a+i+sle+i+++++g+a lcl|FitnessBrowser__psRCH2:GFF269 224 IATDVDGAYLDWGTPQQRRISEAHPDQLQSRG----FAAGSMGPKVQAACEFARNTGNVAVIGSLEQIEAIIKGQA 295 ****************************9988....**************************************** PP TIGR00746 304 Gtvvv 308 Gt+v+ lcl|FitnessBrowser__psRCH2:GFF269 296 GTRVS 300 ***96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (307 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6.58 // [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