Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate WP_028488154.1 Q394_RS0104070 carbamoyl-phosphate synthase small subunit
Query= SwissProt::P0A6F1 (382 letters) >NCBI__GCF_000621325.1:WP_028488154.1 Length = 379 Score = 549 bits (1414), Expect = e-161 Identities = 259/374 (69%), Positives = 306/374 (81%) Query: 1 MIKSALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHI 60 M K ALLVLEDG+ FHGR+IG G GEVVFNT++TGYQEILTDPSYSRQ+VTLTYPHI Sbjct: 1 MNKQALLVLEDGSVFHGRSIGCDGQTTGEVVFNTALTGYQEILTDPSYSRQMVTLTYPHI 60 Query: 61 GNVGTNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTR 120 GNVG N D ES+QVHA GL++RD+P + S++R E L +YL+R+ +VAIADIDTR+LTR Sbjct: 61 GNVGVNQEDCESTQVHAAGLIVRDVPAVYSSWRAEESLPAYLERNKVVAIADIDTRRLTR 120 Query: 121 LLREKGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGG 180 +LREKGAQ GCI+AG N + AL+ AR+FPGL GMDLAKEVT +Y WT+GSW L Sbjct: 121 ILREKGAQRGCIVAGTNLNVEQALDAARSFPGLKGMDLAKEVTAKASYLWTEGSWQLNPA 180 Query: 181 LPEAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSN 240 P + F++VAYD+G K NILRMLVDRGCR+T+VPAQT A DVL +NPDG+FLSN Sbjct: 181 TPRPSTAETAEFNIVAYDYGIKTNILRMLVDRGCRVTVVPAQTPASDVLALNPDGVFLSN 240 Query: 241 GPGDPAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDV 300 GPGDP PCDYAI+AI+ LE +P FGICLGHQLL LASGAKT+KMKFGHHG NHPV+DV Sbjct: 241 GPGDPEPCDYAISAIRTVLENKVPTFGICLGHQLLGLASGAKTIKMKFGHHGANHPVQDV 300 Query: 301 EKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGP 360 + VMI++QNHGFAVDEA+LP N+R TH+SLFDG+LQGI RTD PA SFQGHPEASPGP Sbjct: 301 DSKRVMISSQNHGFAVDEASLPVNVRATHRSLFDGSLQGIERTDCPALSFQGHPEASPGP 360 Query: 361 HDAAPLFDHFIELI 374 HD AP+FD FI+L+ Sbjct: 361 HDVAPVFDRFIDLM 374 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: 511 Number of extensions: 14 Number of successful extensions: 1 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: 379 Length adjustment: 30 Effective length of query: 352 Effective length of database: 349 Effective search space: 122848 Effective search space used: 122848 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 WP_028488154.1 Q394_RS0104070 (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.7015.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8e-151 488.0 0.0 9.2e-151 487.8 0.0 1.0 1 lcl|NCBI__GCF_000621325.1:WP_028488154.1 Q394_RS0104070 carbamoyl-phospha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000621325.1:WP_028488154.1 Q394_RS0104070 carbamoyl-phosphate synthase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 487.8 0.0 9.2e-151 9.2e-151 1 360 [. 5 375 .. 5 376 .. 0.96 Alignments for each domain: == domain 1 score: 487.8 bits; conditional E-value: 9.2e-151 TIGR01368 1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaesk 69 a lvledG+vf+g+s+g++++++GevvFnT++tGYqEiltDpsY++q+v+ltyp+ign+gvn+ed es+ lcl|NCBI__GCF_000621325.1:WP_028488154.1 5 ALLVLEDGSVFHGRSIGCDGQTTGEVVFNTALTGYQEILTDPSYSRQMVTLTYPHIGNVGVNQEDCEST 73 579****************************************************************** PP TIGR01368 70 kikvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavistek.sekee 137 +++++gl+v+++ + +s++ra+esL ++l+++++vai+++DTR l++ lRekg+++++i++ + + e+ lcl|NCBI__GCF_000621325.1:WP_028488154.1 74 QVHAAGLIVRDVPAVYSSWRAEESLPAYLERNKVVAIADIDTRRLTRILREKGAQRGCIVAGTnLNVEQ 142 **********************************************************99876157999 PP TIGR01368 138 lvekakespkvkevnlvkevstkeayeleq.......k....akkegkklrvvvidlGvKenilreLvk 195 + ++a++ p +k+++l+kev++k y +++ +++e+ + ++v++d+G+K+nilr+Lv+ lcl|NCBI__GCF_000621325.1:WP_028488154.1 143 ALDAARSFPGLKGMDLAKEVTAKASYLWTEgswqlnpAtprpSTAETAEFNIVAYDYGIKTNILRMLVD 211 9****************************987766551566677777889******************* PP TIGR01368 196 rgvevtvvpadtsaeeikklnpdgillsnGPGdPaaveeaietvkklleakiPifGIclGhqllalalg 264 rg++vtvvpa+t+a+++ +lnpdg++lsnGPGdP+ +++ai+ ++++le+k+P+fGIclGhqll+la+g lcl|NCBI__GCF_000621325.1:WP_028488154.1 212 RGCRVTVVPAQTPASDVLALNPDGVFLSNGPGDPEPCDYAISAIRTVLENKVPTFGICLGHQLLGLASG 280 ********************************************************************* PP TIGR01368 265 aktyklkfGhrGaNhpvkdlktgrveitsqNHgyavdeeslkeeelevthvnlnDgtveglehkelpvf 333 akt+k+kfGh+GaNhpv+d++++rv+i+sqNHg+avde+sl+ + +++th++l+Dg+++g+e+++ p++ lcl|NCBI__GCF_000621325.1:WP_028488154.1 281 AKTIKMKFGHHGANHPVQDVDSKRVMISSQNHGFAVDEASLPVN-VRATHRSLFDGSLQGIERTDCPAL 348 ****************************************9876.************************ PP TIGR01368 334 svQyHPeaspGphdteylFdefvelik 360 s Q HPeaspGphd + +Fd+f++l++ lcl|NCBI__GCF_000621325.1:WP_028488154.1 349 SFQGHPEASPGPHDVAPVFDRFIDLMR 375 ************************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (361 nodes) Target sequences: 1 (379 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: 7.83 // [ok]
This GapMind analysis is from Apr 10 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