Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate GFF653 PGA1_c06670 carbamoyl-phosphate synthase small chain
Query= SwissProt::P0A6F1 (382 letters) >FitnessBrowser__Phaeo:GFF653 Length = 387 Score = 380 bits (976), Expect = e-110 Identities = 201/385 (52%), Positives = 260/385 (67%), Gaps = 14/385 (3%) Query: 4 SALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNV 63 +A L L DGT F+G GA G V E+ FNT+MTGYQEI+TDPSY+ QIVT T+PHIGN Sbjct: 10 TACLALADGTIFYGNGFGAYGETVAELCFNTAMTGYQEIMTDPSYAGQIVTFTFPHIGNT 69 Query: 64 GTNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTRLLR 123 G D+E++ A G+V++ P +ASN+R TE+L +L R N +AI IDTR+LTR +R Sbjct: 70 GVTPEDDETADPVAAGMVVKWDPTLASNWRATEELKDWLTRTNRIAIGGIDTRRLTRAIR 129 Query: 124 EKGAQNGCIIAGDNPDAALALE----KARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTG 179 + GA + + +PD +E KAR + GL G+DLAK+VT +++Y W + W Sbjct: 130 QLGAPH--VALAHDPDGNFDIEALVAKAREWSGLEGLDLAKDVTCSQSYRWDEMRWAW-- 185 Query: 180 GLPEAKKEDELPFH-VVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFL 238 PE E P H VVA D+GAKRNILR L GC +T++PA +AE+VL +PDG+FL Sbjct: 186 --PEGYTRQEAPKHKVVAIDYGAKRNILRCLASAGCDVTVLPASATAEEVLAHSPDGVFL 243 Query: 239 SNGPGDPAPC-DYAITAIQKFLET-DIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHP 296 SNGPGDPA +YA+ IQ+ L+T D+P+FGICLGHQ+LALA G KTVKM GHHG NHP Sbjct: 244 SNGPGDPAATGEYAVPMIQQILDTTDLPMFGICLGHQMLALALGGKTVKMNHGHHGANHP 303 Query: 297 VKDVEKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEA 356 VK+ V IT+ NHGFAVD +LP + TH SLFDG+ GI +D+P +S Q HPEA Sbjct: 304 VKENATGKVEITSMNHGFAVDGQSLPDGVEETHVSLFDGSNCGIRISDRPVYSVQHHPEA 363 Query: 357 SPGPHDAAPLFDHFIELIEQYRKTA 381 SPGP D+ LF+ F E + RK+A Sbjct: 364 SPGPQDSFYLFERFAEAMAA-RKSA 387 Lambda K H 0.318 0.135 0.400 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: 477 Number of extensions: 22 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: 382 Length of database: 387 Length adjustment: 30 Effective length of query: 352 Effective length of database: 357 Effective search space: 125664 Effective search space used: 125664 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 (21.7 bits) S2: 50 (23.9 bits)
Align candidate GFF653 PGA1_c06670 (carbamoyl-phosphate synthase small chain)
to HMM TIGR01368 (carA: carbamoyl-phosphate synthase, small subunit (EC 6.3.5.5))
# 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.aa/TIGR01368.hmm # target sequence database: /tmp/gapView.30069.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01368 [M=361] Accession: TIGR01368 Description: CPSaseIIsmall: carbamoyl-phosphate synthase, small subunit 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.8e-135 435.6 0.0 7.8e-135 435.4 0.0 1.0 1 lcl|FitnessBrowser__Phaeo:GFF653 PGA1_c06670 carbamoyl-phosphate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF653 PGA1_c06670 carbamoyl-phosphate synthase small chain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 435.4 0.0 7.8e-135 7.8e-135 1 360 [. 11 382 .. 11 383 .. 0.95 Alignments for each domain: == domain 1 score: 435.4 bits; conditional E-value: 7.8e-135 TIGR01368 1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskkikvkglv 77 a l+l+dGt+f g +fga +e+v+e++FnT+mtGYqEi+tDpsY+gqiv++t p+ign+gv++ed e + ++g+v lcl|FitnessBrowser__Phaeo:GFF653 11 ACLALADGTIFYGNGFGAYGETVAELCFNTAMTGYQEIMTDPSYAGQIVTFTFPHIGNTGVTPEDDETADPVAAGMV 87 5799************************************************************************* PP TIGR01368 78 vkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavistekse...keelvekakespkvkev 151 vk + +sn+ra+e+L+++l++++ +ai g+DTR l++ +R+ g+ + +++++ e lv+ka+e ++++ lcl|FitnessBrowser__Phaeo:GFF653 88 VKWDPTLASNWRATEELKDWLTRTNRIAIGGIDTRRLTRAIRQLGAPHVALAHDPDGnfdIEALVAKAREWSGLEGL 164 *************************************************99998765555899999999******** PP TIGR01368 152 nlvkevstkeayeleq......k..akkegkklrvvvidlGvKenilreLvkrgvevtvvpadtsaeeikklnpdgi 220 +l+k+v++++ y++ + + +++e k++vv+id+G K+nilr+L++ g++vtv+pa+++aee+ + +pdg+ lcl|FitnessBrowser__Phaeo:GFF653 165 DLAKDVTCSQSYRWDEmrwawpEgyTRQEAPKHKVVAIDYGAKRNILRCLASAGCDVTVLPASATAEEVLAHSPDGV 241 ***************976655516567777779******************************************** PP TIGR01368 221 llsnGPGdPaav.eeaietvkkllea.kiPifGIclGhqllalalgaktyklkfGhrGaNhpvkdlktgrveitsqN 295 +lsnGPGdPaa e+a+ +++++l++ ++P+fGIclGhq+lalalg+kt+k++ Gh+GaNhpvk+ +tg+veits N lcl|FitnessBrowser__Phaeo:GFF653 242 FLSNGPGDPAATgEYAVPMIQQILDTtDLPMFGICLGHQMLALALGGKTVKMNHGHHGANHPVKENATGKVEITSMN 318 *********776377899******9879************************************************* PP TIGR01368 296 HgyavdeeslkeeelevthvnlnDgtveglehkelpvfsvQyHPeaspGphdteylFdefvelik 360 Hg+avd +sl+ + +e thv+l+Dg++ g++ ++ pv+svQ+HPeaspGp+d+ ylF++f e+++ lcl|FitnessBrowser__Phaeo:GFF653 319 HGFAVDGQSLPDG-VEETHVSLFDGSNCGIRISDRPVYSVQHHPEASPGPQDSFYLFERFAEAMA 382 *********8855.***********************************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (361 nodes) Target sequences: 1 (387 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: 11.62 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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