Align carbamate kinase (EC 2.7.2.2) (characterized)
to candidate WP_053939150.1 WG78_RS17575 carbamate kinase
Query= BRENDA::A0A0H3BY05 (316 letters) >NCBI__GCF_001294205.1:WP_053939150.1 Length = 319 Score = 261 bits (667), Expect = 2e-74 Identities = 151/321 (47%), Positives = 197/321 (61%), Gaps = 8/321 (2%) Query: 1 MTKQKIVVALGGNAILSTD--ASAKAQQEALISTSKSLVKLIKEGHEVIVTHGNGPQVGN 58 M + VVA+GGNA++ D S Q EA+I + +V LI+ G V++THGNGPQVG Sbjct: 1 MKPRLAVVAVGGNALIRDDQHTSIPDQYEAVIESVSHIVPLIEAGWNVVLTHGNGPQVGF 60 Query: 59 LLLQQAAADSEKNPAMPLDTCVAMTEGSIGFWLVNALDNELQAQGIQKEVAAVVTQVIVD 118 +L + A E P +PLD V T+G+IG+ AL NELQ +G+ K V +VTQ V Sbjct: 61 ILRRSELAALEVAP-VPLDYAVGDTQGAIGYMFQKALTNELQRRGLIKPVITLVTQTRVS 119 Query: 119 AKDPAFENPTKPIGPFLTEEDAKKQMAESGASFKEDAGRGWRKVVPSPKPVGIKEANVIR 178 DPAF NP KP+G FL E+ A+ + E G + EDAGRGWR+ V SP+P I E+ +I Sbjct: 120 LSDPAFRNPAKPVGAFLDEDTARIRQRELGWTVMEDAGRGWRRTVASPQPQEILESGLIG 179 Query: 179 SLVDSGVVVVSAGGGGVPVVEDATSKSLTGVEAVIDKDFASQTLSELVDADLFIVLTGVD 238 LV+ G VV++ GGGG+PVV D + L GVEAVIDKD AS L+ + ADL ++ TGV+ Sbjct: 180 QLVEQGCVVIACGGGGIPVVRD-EHQQLQGVEAVIDKDLASALLATQLGADLLLIPTGVE 238 Query: 239 NVYINFNKPDQAKLEEVTVSQMKEYITQDQFAPGSMLPKVEAAIAFVENKPN----AKAI 294 V INF KPDQ L ++++ + + I Q QF GSMLPKVEA + FVE A + Sbjct: 239 QVAINFGKPDQQWLNQLSLEEAQALIEQGQFGAGSMLPKVEAILGFVEQSRQQGKAASGL 298 Query: 295 ITSLENIDNVLSANAGTQIIA 315 ITS I LS GT I A Sbjct: 299 ITSPAAIGRALSRETGTWINA 319 Lambda K H 0.311 0.129 0.349 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: 238 Number of extensions: 11 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: 316 Length of database: 319 Length adjustment: 27 Effective length of query: 289 Effective length of database: 292 Effective search space: 84388 Effective search space used: 84388 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.8 bits) S2: 48 (23.1 bits)
Align candidate WP_053939150.1 WG78_RS17575 (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.44393.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.9e-112 360.2 0.1 4.4e-112 360.1 0.1 1.0 1 NCBI__GCF_001294205.1:WP_053939150.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001294205.1:WP_053939150.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 360.1 0.1 4.4e-112 4.4e-112 3 307 .. 6 317 .. 4 319 .] 0.95 Alignments for each domain: == domain 1 score: 360.1 bits; conditional E-value: 4.4e-112 TIGR00746 3 vvvaLGGnallqrgekasaeeqrknvekaakqlvklakrgyelvithGngPqvGalllqne.aadsvpakPld 74 vva+GGnal++ ++++s+ +q+++v ++++++v l+++g ++v+thGngPqvG +l ++e aa +v++ Pld NCBI__GCF_001294205.1:WP_053939150.1 6 AVVAVGGNALIRDDQHTSIPDQYEAVIESVSHIVPLIEAGWNVVLTHGNGPQVGFILRRSElAALEVAPVPLD 78 69****************************************************998876625556******* PP TIGR00746 75 vlgaesqgliGYllqqalkeelakeglekkvatvltqvivdekDeaFqnPtkpigpfydeeeakrlaaekgai 147 ++ +qg iGY++q+al++el+++gl k+v+t++tq+ v+ D+aF+nP kp+g f+de++a+ ++e g++ NCBI__GCF_001294205.1:WP_053939150.1 79 YAVGDTQGAIGYMFQKALTNELQRRGLIKPVITLVTQTRVSLSDPAFRNPAKPVGAFLDEDTARIRQRELGWT 151 ************************************************************************* PP TIGR00746 148 lkedagrgwRrvvpsPkPkeiveaeviktLvekgvivissgGGGvPvvkdgke.lkGveaviDkDlasekLae 219 + edagrgwRr v+sP+P+ei+e+ i +Lve+g +vi++gGGG+Pvv+d+++ l+GveaviDkDlas++La+ NCBI__GCF_001294205.1:WP_053939150.1 152 VMEDAGRGWRRTVASPQPQEILESGLIGQLVEQGCVVIACGGGGIPVVRDEHQqLQGVEAVIDKDLASALLAT 224 ************************************************988655******************* PP TIGR00746 220 evnaDilviltdvdavyvnygkpdekkleevkveeleelakdgefaaGsmgPkveaaiefves...rgk..ka 287 +++aD l+i t+v++v++n+gkpd+++l+++++ee+++l+++g+f+aGsm+Pkvea+ fve+ +gk + NCBI__GCF_001294205.1:WP_053939150.1 225 QLGADLLLIPTGVEQVAINFGKPDQQWLNQLSLEEAQALIEQGQFGAGSMLPKVEAILGFVEQsrqQGKaaSG 297 *************************************************************752226774445 PP TIGR00746 288 iitslekivealegkaGtvv 307 +its++ i al ++Gt + NCBI__GCF_001294205.1:WP_053939150.1 298 LITSPAAIGRALSRETGTWI 317 9*****************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (319 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.05 # Mc/sec: 1.88 // [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