Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate Ga0059261_4243 Ga0059261_4243 carbamoyl-phosphate synthase, small subunit
Query= SwissProt::P0A6F1 (382 letters) >FitnessBrowser__Korea:Ga0059261_4243 Length = 390 Score = 379 bits (973), Expect = e-110 Identities = 199/376 (52%), Positives = 249/376 (66%), Gaps = 4/376 (1%) Query: 4 SALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNV 63 + +LVL G GR GA G A GEV F+T+MTGYQEI+TDPS++ Q++ T+PHIGNV Sbjct: 14 TGVLVLASGEVIWGRGFGAEGHAAGEVCFHTAMTGYQEIMTDPSFAGQMICFTFPHIGNV 73 Query: 64 GTNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTRLLR 123 G N D E+ HA G+++R+ SNFR+ E L ++K+H+ + +A IDTR LTR +R Sbjct: 74 GANPDDVEADNPHALGMIVREDVTEPSNFRSVERLDDWMKQHDRIGLAGIDTRALTRRIR 133 Query: 124 EKGAQNGCII--AGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGGL 181 +GA NG I A D LE+ARA+PGL GMDLA VTT + W G W L G Sbjct: 134 GQGAPNGVIAHSASGEFDIPWLLERARAWPGLEGMDLAITVTTETHFGWEGGVWRLGFGY 193 Query: 182 PEAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSNG 241 E ED P HVVA D+G+K NI R LV G ++T++PA +AE VL NPDGIFLSNG Sbjct: 194 GEEGAEDGRP-HVVAIDYGSKHNIFRNLVQAGAKVTVLPATATAEQVLSFNPDGIFLSNG 252 Query: 242 PGDPAPC-DYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDV 300 PGDPA +YA+ I++ LET P+FGICLGHQLL LA GA+T KM GH G NHPVK + Sbjct: 253 PGDPAATGEYAVPVIRELLETKKPLFGICLGHQLLGLAVGAQTTKMFQGHRGANHPVKRL 312 Query: 301 EKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGP 360 V IT+ NHGFA+D ATLPAN+ TH SLFDG+ GI AFS Q HPEASPGP Sbjct: 313 SDGAVEITSMNHGFAIDRATLPANVTETHVSLFDGSNCGIEIDGGRAFSVQYHPEASPGP 372 Query: 361 HDAAPLFDHFIELIEQ 376 D+ LF+ F+ ++ Q Sbjct: 373 QDSFYLFERFVGMLGQ 388 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: 475 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: 390 Length adjustment: 30 Effective length of query: 352 Effective length of database: 360 Effective search space: 126720 Effective search space used: 126720 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 Ga0059261_4243 Ga0059261_4243 (carbamoyl-phosphate synthase, small subunit)
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.26612.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-131 424.3 0.0 2.2e-131 424.1 0.0 1.0 1 lcl|FitnessBrowser__Korea:Ga0059261_4243 Ga0059261_4243 carbamoyl-phospha Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Korea:Ga0059261_4243 Ga0059261_4243 carbamoyl-phosphate synthase, small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 424.1 0.0 2.2e-131 2.2e-131 2 358 .. 16 385 .. 15 388 .. 0.95 Alignments for each domain: == domain 1 score: 424.1 bits; conditional E-value: 2.2e-131 TIGR01368 2 tlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskk 70 +lvl+ G+v+ g++fgae++++Gev+F+T+mtGYqEi+tDps++gq++ +t p+ign+g n++d+e+++ lcl|FitnessBrowser__Korea:Ga0059261_4243 16 VLVLASGEVIWGRGFGAEGHAAGEVCFHTAMTGYQEIMTDPSFAGQMICFTFPHIGNVGANPDDVEADN 84 69******************************************************************* PP TIGR01368 71 ikvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavistekse...ke 136 +++ g++v+e +e+sn+r+ e L++++k+++ ++++g+DTRal++++R +g+ ++vi++++s lcl|FitnessBrowser__Korea:Ga0059261_4243 85 PHALGMIVREDVTEPSNFRSVERLDDWMKQHDRIGLAGIDTRALTRRIRGQGAPNGVIAHSASGefdIP 153 ***********************************************************9987744455 PP TIGR01368 137 elvekakespkvkevnlvkevstkeayeleq..........kakkegkklrvvvidlGvKenilreLvk 195 l e+a++ p +++++l+ +v+t+++ +e ++ +e+ + +vv+id+G K+ni r+Lv+ lcl|FitnessBrowser__Korea:Ga0059261_4243 154 WLLERARAWPGLEGMDLAITVTTETHFGWEGgvwrlgfgygEEGAEDGRPHVVAIDYGSKHNIFRNLVQ 222 6889999**********************9988877766653555566679****************** PP TIGR01368 196 rgvevtvvpadtsaeeikklnpdgillsnGPGdPaav.eeaietvkklleakiPifGIclGhqllalal 263 g++vtv+pa+++ae++ ++npdgi+lsnGPGdPaa e+a+ +++lle+k+P+fGIclGhqll+la+ lcl|FitnessBrowser__Korea:Ga0059261_4243 223 AGAKVTVLPATATAEQVLSFNPDGIFLSNGPGDPAATgEYAVPVIRELLETKKPLFGICLGHQLLGLAV 291 **********************************876377899************************** PP TIGR01368 264 gaktyklkfGhrGaNhpvkdlktgrveitsqNHgyavdeeslkeeelevthvnlnDgtveglehkelpv 332 ga+t k+ GhrGaNhpvk l++g veits NHg+a+d+++l+++ ++ thv+l+Dg++ g+e ++ lcl|FitnessBrowser__Korea:Ga0059261_4243 292 GAQTTKMFQGHRGANHPVKRLSDGAVEITSMNHGFAIDRATLPAN-VTETHVSLFDGSNCGIEIDGGRA 359 *****************************************8866.99********************* PP TIGR01368 333 fsvQyHPeaspGphdteylFdefvel 358 fsvQyHPeaspGp+d+ ylF++fv + lcl|FitnessBrowser__Korea:Ga0059261_4243 360 FSVQYHPEASPGPQDSFYLFERFVGM 385 ***********************976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (361 nodes) Target sequences: 1 (390 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: 10.24 // [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