Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate Dsui_3065 Dsui_3065 carbamoyl-phosphate synthase, small subunit
Query= SwissProt::P0A6F1 (382 letters) >FitnessBrowser__PS:Dsui_3065 Length = 382 Score = 506 bits (1304), Expect = e-148 Identities = 260/380 (68%), Positives = 293/380 (77%), Gaps = 9/380 (2%) Query: 5 ALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNVG 64 ALL L DGT F G AIGA G+ GEVVFNT+MTGYQEILTDPSY RQIVTLTYPHIGN G Sbjct: 10 ALLALADGTVFRGYAIGAEGTTSGEVVFNTAMTGYQEILTDPSYCRQIVTLTYPHIGNTG 69 Query: 65 TNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTRLLRE 124 N D ES A GLVIRDLP+ ASN+R + L YLK+H +VAIA IDTRKLTR+LRE Sbjct: 70 CNAEDFESRANFAAGLVIRDLPIRASNWRIEQTLPDYLKQHGVVAIAGIDTRKLTRILRE 129 Query: 125 KGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTG--GLP 182 KGAQ GCIIAG D A AL +ARAFPGL GMDLAK V+ Y +++G WTL G P Sbjct: 130 KGAQAGCIIAGV-ADEAKALAEARAFPGLAGMDLAKVVSVDSPYQFSEGEWTLKGYAAAP 188 Query: 183 EAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSNGP 242 AK F VVAYD+G K NILRML RGC +T+VPAQT A +VLK PDG+FLSNGP Sbjct: 189 AAK------FKVVAYDYGVKTNILRMLAARGCDVTVVPAQTPAAEVLKYKPDGVFLSNGP 242 Query: 243 GDPAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDVEK 302 GDP PCDYAITAI++ L +P +GICLGHQLLALASGAKT+KMKFGHHG NHPVKD++ Sbjct: 243 GDPEPCDYAITAIREILAAGVPTYGICLGHQLLALASGAKTLKMKFGHHGANHPVKDLDT 302 Query: 303 NVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGPHD 362 N V+IT+QNHGFAVD TLPAN+R TH SLFDG+LQGI RTD PAFSFQGHPEASPGPHD Sbjct: 303 NQVLITSQNHGFAVDADTLPANVRATHVSLFDGSLQGIARTDVPAFSFQGHPEASPGPHD 362 Query: 363 AAPLFDHFIELIEQYRKTAK 382 A LFD FI+L++ + K Sbjct: 363 VAYLFDRFIKLMQDKKAEGK 382 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: 504 Number of extensions: 12 Number of successful extensions: 3 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: 382 Length adjustment: 30 Effective length of query: 352 Effective length of database: 352 Effective search space: 123904 Effective search space used: 123904 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 Dsui_3065 Dsui_3065 (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.19800.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-152 493.6 0.0 1.8e-152 493.4 0.0 1.0 1 lcl|FitnessBrowser__PS:Dsui_3065 Dsui_3065 carbamoyl-phosphate sy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PS:Dsui_3065 Dsui_3065 carbamoyl-phosphate synthase, small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 493.4 0.0 1.8e-152 1.8e-152 1 360 [. 10 375 .. 10 376 .. 0.98 Alignments for each domain: == domain 1 score: 493.4 bits; conditional E-value: 1.8e-152 TIGR01368 1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskkikvkglv 77 a l+l+dGtvf+g+++gae+++ GevvFnT+mtGYqEiltDpsY +qiv+ltyp+ign+g+n+ed+es+ ++glv lcl|FitnessBrowser__PS:Dsui_3065 10 ALLALADGTVFRGYAIGAEGTTSGEVVFNTAMTGYQEILTDPSYCRQIVTLTYPHIGNTGCNAEDFESRANFAAGLV 86 579************************************************************************** PP TIGR01368 78 vkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavisteksekeelvekakespkvkevnlv 154 +++l ++sn+r +++L ++lk++g+vai+g+DTR+l++ lRekg+++++i + ++ ++ ++a++ p +++++l+ lcl|FitnessBrowser__PS:Dsui_3065 87 IRDLPIRASNWRIEQTLPDYLKQHGVVAIAGIDTRKLTRILREKGAQAGCIIAGVADEAKALAEARAFPGLAGMDLA 163 ***************************************************************************** PP TIGR01368 155 kevstkeayeleq.....k..akkegkklrvvvidlGvKenilreLvkrgvevtvvpadtsaeeikklnpdgillsn 224 k vs++++y++++ k a + k +vv++d+GvK+nilr+L++rg++vtvvpa+t+a+e+ k++pdg++lsn lcl|FitnessBrowser__PS:Dsui_3065 164 KVVSVDSPYQFSEgewtlKgyAAAPAAKFKVVAYDYGVKTNILRMLAARGCDVTVVPAQTPAAEVLKYKPDGVFLSN 240 ************97665526677888889************************************************ PP TIGR01368 225 GPGdPaaveeaietvkklleakiPifGIclGhqllalalgaktyklkfGhrGaNhpvkdlktgrveitsqNHgyavd 301 GPGdP+ +++ai+ ++++l a +P++GIclGhqllala+gakt+k+kfGh+GaNhpvkdl+t++v itsqNHg+avd lcl|FitnessBrowser__PS:Dsui_3065 241 GPGDPEPCDYAITAIREILAAGVPTYGICLGHQLLALASGAKTLKMKFGHHGANHPVKDLDTNQVLITSQNHGFAVD 317 ***************************************************************************** PP TIGR01368 302 eeslkeeelevthvnlnDgtveglehkelpvfsvQyHPeaspGphdteylFdefvelik 360 ++l+++ +++thv+l+Dg+++g++++++p+fs Q HPeaspGphd +ylFd+f++l++ lcl|FitnessBrowser__PS:Dsui_3065 318 ADTLPAN-VRATHVSLFDGSLQGIARTDVPAFSFQGHPEASPGPHDVAYLFDRFIKLMQ 375 ***8866.************************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (361 nodes) Target sequences: 1 (382 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 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 12.15 // [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