Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate WP_057509127.1 ABB28_RS13575 carbamoyl-phosphate synthase small subunit
Query= SwissProt::P0A6F1 (382 letters) >NCBI__GCF_001431535.1:WP_057509127.1 Length = 376 Score = 488 bits (1255), Expect = e-142 Identities = 239/378 (63%), Positives = 291/378 (76%), Gaps = 7/378 (1%) Query: 1 MIKSALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHI 60 M ++A+LVLEDGT F G ++GA G +VGEVVFNT+MTGYQE+LTDPSY+RQ+VTLTYPHI Sbjct: 1 MTQAAILVLEDGTVFEGESVGAPGLSVGEVVFNTAMTGYQEVLTDPSYARQMVTLTYPHI 60 Query: 61 GNVGTNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTR 120 GN G D D E+S+V + GL++RD+P S++R+ L +L + +VAI+ IDTRKLTR Sbjct: 61 GNTGMTDQDNEASKVWSAGLIVRDVPRRPSSWRSQVSLQDWLLQRGVVAISGIDTRKLTR 120 Query: 121 LLREKGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGG 180 +LREKGAQNG ++AG+ ALE AR+FPGL GMDLAK V+T Y W +G L Sbjct: 121 ILREKGAQNGALMAGEGISVEKALEAARSFPGLKGMDLAKVVSTETTYQWNEGQLDL--- 177 Query: 181 LPEAKKEDELP--FHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFL 238 +A +P + VVAYD+G K NILRML +RGC +T+VPAQT A DVL + PDG+FL Sbjct: 178 --DANAFVSVPSQYKVVAYDYGVKTNILRMLAERGCDVTVVPAQTPAADVLALKPDGVFL 235 Query: 239 SNGPGDPAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVK 298 SNGPGDP PCDYAI+AI+ L+ +P FGICLGHQLLALASGAKT+KM GHHG NHPV+ Sbjct: 236 SNGPGDPEPCDYAISAIKTVLDARVPTFGICLGHQLLALASGAKTLKMGHGHHGANHPVQ 295 Query: 299 DVEKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASP 358 D++ VMIT+QNHGFAVDEATLP LRVTH+SLFDGT QGI RTD PAFSFQGHPEASP Sbjct: 296 DLDSGRVMITSQNHGFAVDEATLPTTLRVTHRSLFDGTNQGIARTDVPAFSFQGHPEASP 355 Query: 359 GPHDAAPLFDHFIELIEQ 376 GP D PLFD F+ L+ + Sbjct: 356 GPTDVGPLFDRFVTLMAE 373 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: 15 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: 376 Length adjustment: 30 Effective length of query: 352 Effective length of database: 346 Effective search space: 121792 Effective search space used: 121792 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_057509127.1 ABB28_RS13575 (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.19575.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-147 475.8 0.0 4.8e-147 475.6 0.0 1.0 1 lcl|NCBI__GCF_001431535.1:WP_057509127.1 ABB28_RS13575 carbamoyl-phosphat Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001431535.1:WP_057509127.1 ABB28_RS13575 carbamoyl-phosphate synthase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 475.6 0.0 4.8e-147 4.8e-147 1 360 [. 5 372 .. 5 373 .. 0.96 Alignments for each domain: == domain 1 score: 475.6 bits; conditional E-value: 4.8e-147 TIGR01368 1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaesk 69 a+lvledGtvfeg+s+ga++ vGevvFnT+mtGYqE+ltDpsY++q+v+ltyp+ign+g++++d+e++ lcl|NCBI__GCF_001431535.1:WP_057509127.1 5 AILVLEDGTVFEGESVGAPGLSVGEVVFNTAMTGYQEVLTDPSYARQMVTLTYPHIGNTGMTDQDNEAS 73 68******************************************************************* PP TIGR01368 70 kikvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavistek.sekee 137 k++ +gl+v+++ +++s++r++ sL+++l ++g+vai g+DTR+l++ lRekg++++++++ + ++ e+ lcl|NCBI__GCF_001431535.1:WP_057509127.1 74 KVWSAGLIVRDVPRRPSSWRSQVSLQDWLLQRGVVAISGIDTRKLTRILREKGAQNGALMAGEgISVEK 142 ********************************************************9998765267999 PP TIGR01368 138 lvekakespkvkevnlvkevstkeayeleq.......k.akkegkklrvvvidlGvKenilreLvkrgv 198 + e+a++ p +k+++l+k vst+++y++++ + + ++++vv++d+GvK+nilr+L++rg+ lcl|NCBI__GCF_001431535.1:WP_057509127.1 143 ALEAARSFPGLKGMDLAKVVSTETTYQWNEgqldldaNaFVSVPSQYKVVAYDYGVKTNILRMLAERGC 211 *****************************9766655424334445579********************* PP TIGR01368 199 evtvvpadtsaeeikklnpdgillsnGPGdPaaveeaietvkklleakiPifGIclGhqllalalgakt 267 +vtvvpa+t+a+++ +l+pdg++lsnGPGdP+ +++ai+ +k++l+a++P+fGIclGhqllala+gakt lcl|NCBI__GCF_001431535.1:WP_057509127.1 212 DVTVVPAQTPAADVLALKPDGVFLSNGPGDPEPCDYAISAIKTVLDARVPTFGICLGHQLLALASGAKT 280 ********************************************************************* PP TIGR01368 268 yklkfGhrGaNhpvkdlktgrveitsqNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsvQ 336 +k+ Gh+GaNhpv+dl++grv+itsqNHg+avde++l+ ++l+vth++l+Dgt++g++++++p+fs Q lcl|NCBI__GCF_001431535.1:WP_057509127.1 281 LKMGHGHHGANHPVQDLDSGRVMITSQNHGFAVDEATLP-TTLRVTHRSLFDGTNQGIARTDVPAFSFQ 348 ************************************987.66*************************** PP TIGR01368 337 yHPeaspGphdteylFdefvelik 360 HPeaspGp+d lFd+fv+l++ lcl|NCBI__GCF_001431535.1:WP_057509127.1 349 GHPEASPGPTDVGPLFDRFVTLMA 372 ********************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (361 nodes) Target sequences: 1 (376 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: 9.12 // [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