Align Carbamate kinase; EC 2.7.2.2 (characterized, see rationale)
to candidate GFF4048 HP15_3988 bacterial carbamate kinase
Query= uniprot:P13982 (310 letters) >FitnessBrowser__Marino:GFF4048 Length = 302 Score = 346 bits (888), Expect = e-100 Identities = 183/304 (60%), Positives = 225/304 (74%), Gaps = 3/304 (0%) Query: 1 MRIVVALGGNALLRRGEPMTADNQRENVRIAAEQIAKVA-PGNELVIAHGNGPQVGLLAL 59 M +V ALGGNALL+RGEP+TA+ QR NV+IAA +A V G+ LV+ HGNGPQVGLLAL Sbjct: 1 MLVVAALGGNALLKRGEPLTAEVQRNNVQIAARSLAAVVRAGHNLVVTHGNGPQVGLLAL 60 Query: 60 QGAAYDKVSPYPLDVLGAETEGMIGYMIEQEMGNLLPFEVPFATILTQVEVDGKDPAFQN 119 QGA+Y YPLDVLGAETEGMIGYMIEQE+ N L + P AT+LTQV VD +DPAF+ Sbjct: 61 QGASYKPDEAYPLDVLGAETEGMIGYMIEQELENALGHDRPVATLLTQVVVDPRDPAFEK 120 Query: 120 PTKPIGPVYSREEAERLAAEKGWSIAPDGDKFRRVVPSPRPKRIFEIRPVKWLLEKGTIV 179 PTK +GPVY REE ER AA GWSIAPDGDK+RRVVPSP+P I ++R +K LL++G +V Sbjct: 121 PTKFVGPVYDREEGERRAAAAGWSIAPDGDKWRRVVPSPKPLEIPDMRVLKLLLDQGVVV 180 Query: 180 ICAGGGGIPTMYDEAGKKLSGVEAVIDKDLCSSLLAQELVADILIIATDVDAAYVDWGKP 239 +CAGGGGIP + + G + G+EAVIDKD S+LLA++L AD L++ TDV+A Y D+G Sbjct: 181 VCAGGGGIPVLRRDDG-SMVGIEAVIDKDAASALLARQLGADALLLLTDVEAVYRDFGTD 239 Query: 240 TQKAIAQAHPDELERLGFAAGSMGPKVQAAIEFARATGKDAVIGSLADIVAITEGKAGTR 299 A+++ E L AGSMGPK+QAA +FA+A G IG L D VAI EG AGTR Sbjct: 240 RSTALSELTVSEARALEMPAGSMGPKLQAACDFAQAGGISG-IGRLQDAVAILEGSAGTR 298 Query: 300 VSTR 303 VS + Sbjct: 299 VSAK 302 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: 324 Number of extensions: 17 Number of successful extensions: 4 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: 302 Length adjustment: 27 Effective length of query: 283 Effective length of database: 275 Effective search space: 77825 Effective search space used: 77825 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 GFF4048 HP15_3988 (bacterial 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.19503.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-118 381.4 0.0 1.5e-118 381.3 0.0 1.0 1 lcl|FitnessBrowser__Marino:GFF4048 HP15_3988 bacterial carbamate ki Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF4048 HP15_3988 bacterial carbamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 381.3 0.0 1.5e-118 1.5e-118 3 308 .. 3 300 .. 1 301 [. 0.97 Alignments for each domain: == domain 1 score: 381.3 bits; conditional E-value: 1.5e-118 TIGR00746 3 vvvaLGGnallqrgekasaeeqrknvekaakqlvklakrgyelvithGngPqvGalllqneaadsvpakPldvlg 77 vv aLGGnall+rge ++ae qr+nv++aa++l++++++g++lv+thGngPqvG l+lq + ++ +a+Pldvlg lcl|FitnessBrowser__Marino:GFF4048 3 VVAALGGNALLKRGEPLTAEVQRNNVQIAARSLAAVVRAGHNLVVTHGNGPQVGLLALQGASYKPDEAYPLDVLG 77 7999*********************************************************************** PP TIGR00746 78 aesqgliGYllqqalkeelakeglekkvatvltqvivdekDeaFqnPtkpigpfydeeeakrlaaekgailkeda 152 ae++g+iGY+++q+l+++l ++vat+ltqv+vd+ D+aF++Ptk++gp+yd+ee +r aa++g++++ + lcl|FitnessBrowser__Marino:GFF4048 78 AETEGMIGYMIEQELENALG---HDRPVATLLTQVVVDPRDPAFEKPTKFVGPVYDREEGERRAAAAGWSIAP-D 148 *****************999...99************************************************.9 PP TIGR00746 153 grgwRrvvpsPkPkeiveaeviktLvekgvivissgGGGvPvvk.dgkelkGveaviDkDlasekLaeevnaDil 226 g++wRrvvpsPkP+ei +++v+k L+++gv+v+++gGGG+Pv + d+ ++ G+eaviDkD as++La++++aD+l lcl|FitnessBrowser__Marino:GFF4048 149 GDKWRRVVPSPKPLEIPDMRVLKLLLDQGVVVVCAGGGGIPVLRrDDGSMVGIEAVIDKDAASALLARQLGADAL 223 ******************************************8626667************************** PP TIGR00746 227 viltdvdavyvnygkpdekkleevkveeleelakdgefaaGsmgPkveaaiefvesrgkkaiitslekivealeg 301 ++ltdv+avy+++g++ +l+e++v+e+++l+ + aGsmgPk++aa +f++++g + i++l+++v++leg lcl|FitnessBrowser__Marino:GFF4048 224 LLLTDVEAVYRDFGTDRSTALSELTVSEARALE----MPAGSMGPKLQAACDFAQAGGI-SGIGRLQDAVAILEG 293 ********************************9....9*****************9886.679************ PP TIGR00746 302 kaGtvvv 308 aGt+v+ lcl|FitnessBrowser__Marino:GFF4048 294 SAGTRVS 300 *****97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (302 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: 7.66 // [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