Align Carbamate kinase; EC 2.7.2.2 (characterized, see rationale)
to candidate SMa0697 SMa0697 carbamate kinase
Query= uniprot:P13982 (310 letters) >FitnessBrowser__Smeli:SMa0697 Length = 324 Score = 398 bits (1023), Expect = e-116 Identities = 196/311 (63%), Positives = 244/311 (78%), Gaps = 3/311 (0%) Query: 1 MRIVVALGGNALLRRGEPMTADNQRENVRIAAEQIAKVAPGNELVIAHGNGPQVGLLALQ 60 MR+V+ALGGNALL+RGEPMTA+ QR+N++IAAE IA +A +++V+ HGNGPQVGLLALQ Sbjct: 1 MRVVIALGGNALLKRGEPMTAEVQRQNIKIAAEAIAPIAAEHQIVVTHGNGPQVGLLALQ 60 Query: 61 GAAYDKVSPYPLDVLGAETEGMIGYMIEQEMGNLLPFEVPFATILTQVEVDGKDPAFQNP 120 G+AY YPLD+LGAETEGMIGYM+EQE+GN+LPFEVP ATILT VEVDG DP FQNP Sbjct: 61 GSAYKPEEAYPLDILGAETEGMIGYMLEQELGNVLPFEVPLATILTMVEVDGNDPGFQNP 120 Query: 121 TKPIGPVYSREEAERLAAEKGWSIAPDGDKFRRVVPSPRPKRIFEIRPVKWLLEKGTIVI 180 TK +GPVY EA L +KGW DG+K+RRVV SP P+RIFE+RP++WLL+KG +VI Sbjct: 121 TKFVGPVYDASEAGELHQQKGWVFKQDGNKWRRVVASPIPRRIFELRPIQWLLDKGAVVI 180 Query: 181 CAGGGGIPTMYDEAGKK--LSGVEAVIDKDLCSSLLAQELVADILIIATDVDAAYVDWGK 238 CAGGGGIPTMY E GK+ L GVEAVIDKDLCS+LLA+++ AD+LI+ATD +A + WG Sbjct: 181 CAGGGGIPTMY-ERGKERTLIGVEAVIDKDLCSALLARDIEADLLILATDAEAVFTGWGT 239 Query: 239 PTQKAIAQAHPDELERLGFAAGSMGPKVQAAIEFARATGKDAVIGSLADIVAITEGKAGT 298 P +KAI + +P L F AGSMGPKV+AA F ATG+ A IG+LADI A+ + GT Sbjct: 240 PERKAIFKTNPRRLGEFSFPAGSMGPKVEAACHFVNATGRVAAIGALADIPAMVRAERGT 299 Query: 299 RVSTRKAGIEY 309 +S+ + I + Sbjct: 300 IISSSFSDITW 310 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: 398 Number of extensions: 17 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: 324 Length adjustment: 27 Effective length of query: 283 Effective length of database: 297 Effective search space: 84051 Effective search space used: 84051 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 SMa0697 SMa0697 (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.14635.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.6e-117 375.5 0.0 9.8e-117 375.3 0.0 1.0 1 lcl|FitnessBrowser__Smeli:SMa0697 SMa0697 carbamate kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SMa0697 SMa0697 carbamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 375.3 0.0 9.8e-117 9.8e-117 1 308 [. 1 302 [. 1 303 [. 0.98 Alignments for each domain: == domain 1 score: 375.3 bits; conditional E-value: 9.8e-117 TIGR00746 1 kkvvvaLGGnallqrgekasaeeqrknvekaakqlvklakrgyelvithGngPqvGalllqneaadsvpakPldvl 76 ++vv+aLGGnall+rge ++ae qr+n+++aa++++ +a+ +++v+thGngPqvG l+lq +a++ +a+Pld+l lcl|FitnessBrowser__Smeli:SMa0697 1 MRVVIALGGNALLKRGEPMTAEVQRQNIKIAAEAIAPIAA-EHQIVVTHGNGPQVGLLALQGSAYKPEEAYPLDIL 75 589***********************************99.9********************************** PP TIGR00746 77 gaesqgliGYllqqalkeelakeglekkvatvltqvivdekDeaFqnPtkpigpfydeeeakrlaaekgailkeda 152 gae++g+iGY+l+q+l ++l+ +e ++at+lt v+vd +D+ FqnPtk++gp+yd ea +l ++kg+ +k+ + lcl|FitnessBrowser__Smeli:SMa0697 76 GAETEGMIGYMLEQELGNVLP---FEVPLATILTMVEVDGNDPGFQNPTKFVGPVYDASEAGELHQQKGWVFKQ-D 147 *********************...**************************************************.8 PP TIGR00746 153 grgwRrvvpsPkPkeiveaeviktLvekgvivissgGGGvPvvkdgke...lkGveaviDkDlasekLaeevnaDi 225 g++wRrvv+sP P++i+e + i++L++kg +vi++gGGG+P++++ + l GveaviDkDl+s++La++++aD lcl|FitnessBrowser__Smeli:SMa0697 148 GNKWRRVVASPIPRRIFELRPIQWLLDKGAVVICAGGGGIPTMYERGKertLIGVEAVIDKDLCSALLARDIEADL 223 99*****************************************99655466************************* PP TIGR00746 226 lviltdvdavyvnygkpdekkleevkveeleelakdgefaaGsmgPkveaaiefvesrgkkaiitslekivealeg 301 l+++td++av++ +g+p+ k++ + ++ l e+ f aGsmgPkveaa +fv+++g a i++l++i +++ lcl|FitnessBrowser__Smeli:SMa0697 224 LILATDAEAVFTGWGTPERKAIFKTNPRRLGEFS----FPAGSMGPKVEAACHFVNATGRVAAIGALADIPAMVRA 295 *********************************9....************************************** PP TIGR00746 302 kaGtvvv 308 + Gt+++ lcl|FitnessBrowser__Smeli:SMa0697 296 ERGTIIS 302 ****997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (324 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: 00:00:00.01 # Mc/sec: 7.81 // [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