Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate 6938385 Sama_2504 carbamoyl phosphate synthase small subunit (RefSeq)
Query= SwissProt::P0A6F1 (382 letters) >FitnessBrowser__SB2B:6938385 Length = 381 Score = 619 bits (1595), Expect = 0.0 Identities = 306/382 (80%), Positives = 328/382 (85%), Gaps = 1/382 (0%) Query: 1 MIKSALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHI 60 M KSALLVLEDGT F G AIGA G AVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHI Sbjct: 1 MTKSALLVLEDGTLFSGTAIGADGIAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHI 60 Query: 61 GNVGTNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTR 120 GN GTND D ESS VHA GL+IRDLPLIAS+FR+T+ LS YLK +N+V IADIDTRKLTR Sbjct: 61 GNTGTNDEDTESSAVHACGLIIRDLPLIASSFRSTQSLSDYLKANNVVGIADIDTRKLTR 120 Query: 121 LLREKGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGG 180 +LREKGAQ GCI+ GD D+ AL A+AFPGL GMDLAKEVTTAE Y W GSW L GG Sbjct: 121 ILREKGAQAGCILVGDL-DSDKALAAAKAFPGLKGMDLAKEVTTAERYQWRSGSWRLEGG 179 Query: 181 LPEAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSN 240 LP E EL F VVAYD+G K NILRMLVDRGC +T+VPA+T A +VL MNPDG+FLSN Sbjct: 180 LPSDTPESELKFKVVAYDYGVKTNILRMLVDRGCDVTVVPAKTPASEVLAMNPDGVFLSN 239 Query: 241 GPGDPAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDV 300 GPGDP PCDYAI AIQ+ L TDIPVFGICLGHQLL LASGAKT+KMKFGHHG NHPV DV Sbjct: 240 GPGDPEPCDYAIAAIQEILTTDIPVFGICLGHQLLGLASGAKTLKMKFGHHGANHPVGDV 299 Query: 301 EKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGP 360 EK VMIT+QNHGFAVDEATLPANL+VTHKSLFDG+LQGIHRTDKPAFSFQGHPEASPGP Sbjct: 300 EKGTVMITSQNHGFAVDEATLPANLKVTHKSLFDGSLQGIHRTDKPAFSFQGHPEASPGP 359 Query: 361 HDAAPLFDHFIELIEQYRKTAK 382 HD APLFDHFIELIE+YRK AK Sbjct: 360 HDCAPLFDHFIELIEEYRKNAK 381 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: 538 Number of extensions: 10 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: 382 Length of database: 381 Length adjustment: 30 Effective length of query: 352 Effective length of database: 351 Effective search space: 123552 Effective search space used: 123552 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 6938385 Sama_2504 (carbamoyl phosphate synthase small subunit (RefSeq))
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.1712.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.1e-154 498.2 0.0 7e-154 498.1 0.0 1.0 1 lcl|FitnessBrowser__SB2B:6938385 Sama_2504 carbamoyl phosphate sy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6938385 Sama_2504 carbamoyl phosphate synthase small subunit (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 498.1 0.0 7e-154 7e-154 1 360 [. 5 374 .. 5 375 .. 0.97 Alignments for each domain: == domain 1 score: 498.1 bits; conditional E-value: 7e-154 TIGR01368 1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskkikvkglv 77 a lvledGt f+g+++ga++ +vGevvFnTsmtGYqEiltDpsY++qiv+ltyp+ign+g+n+ed+es+ +++ gl+ lcl|FitnessBrowser__SB2B:6938385 5 ALLVLEDGTLFSGTAIGADGIAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNTGTNDEDTESSAVHACGLI 81 579************************************************************************** PP TIGR01368 78 vkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavisteksekeelvekakespkvkevnlv 154 +++l +s++r+++sL+++lk +++v+i+++DTR+l++ lRekg+++++i + +++++ ++ak+ p +k+++l+ lcl|FitnessBrowser__SB2B:6938385 82 IRDLPLIASSFRSTQSLSDYLKANNVVGIADIDTRKLTRILREKGAQAGCILVGDLDSDKALAAAKAFPGLKGMDLA 158 ***************************************************************************** PP TIGR01368 155 kevstkeayeleq...........kakkegkklrvvvidlGvKenilreLvkrgvevtvvpadtsaeeikklnpdgi 220 kev+t+e+y++++ ++ +++ k +vv++d+GvK+nilr+Lv+rg++vtvvpa+t+a+e+ ++npdg+ lcl|FitnessBrowser__SB2B:6938385 159 KEVTTAERYQWRSgswrlegglpsDTPESELKFKVVAYDYGVKTNILRMLVDRGCDVTVVPAKTPASEVLAMNPDGV 235 ************988777665553366666679******************************************** PP TIGR01368 221 llsnGPGdPaaveeaietvkklleakiPifGIclGhqllalalgaktyklkfGhrGaNhpvkdlktgrveitsqNHg 297 +lsnGPGdP+ +++ai+ ++++l+++iP+fGIclGhqll+la+gakt+k+kfGh+GaNhpv d+++g+v+itsqNHg lcl|FitnessBrowser__SB2B:6938385 236 FLSNGPGDPEPCDYAIAAIQEILTTDIPVFGICLGHQLLGLASGAKTLKMKFGHHGANHPVGDVEKGTVMITSQNHG 312 ***************************************************************************** PP TIGR01368 298 yavdeeslkeeelevthvnlnDgtveglehkelpvfsvQyHPeaspGphdteylFdefvelik 360 +avde++l+++ l+vth++l+Dg+++g++++++p+fs Q HPeaspGphd + lFd+f+eli+ lcl|FitnessBrowser__SB2B:6938385 313 FAVDEATLPAN-LKVTHKSLFDGSLQGIHRTDKPAFSFQGHPEASPGPHDCAPLFDHFIELIE 374 *******8866.************************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (361 nodes) Target sequences: 1 (381 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: 8.74 // [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