Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate WP_022949935.1 H035_RS0115815 carbamoyl-phosphate synthase small subunit
Query= SwissProt::P0A6F1 (382 letters) >NCBI__GCF_000421465.1:WP_022949935.1 Length = 376 Score = 477 bits (1227), Expect = e-139 Identities = 233/377 (61%), Positives = 286/377 (75%), Gaps = 8/377 (2%) Query: 1 MIKSALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHI 60 M ++A+L LEDGT F G +IG +G VGEVVFNT++TGYQEILTDPSY+RQ+VTLTYPHI Sbjct: 1 MKETAILALEDGTLFQGVSIGGSGCRVGEVVFNTALTGYQEILTDPSYARQLVTLTYPHI 60 Query: 61 GNVGTNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTR 120 GNVG N D ES +HA GL++RD+P +ASN+R TE L++YLKR ++V IADIDTRKLTR Sbjct: 61 GNVGVNPEDVESDYIHAAGLIVRDVPGVASNWRMTESLTAYLKRRDVVGIADIDTRKLTR 120 Query: 121 LLREKGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGG 180 +LR+KGAQ GC+ AG + D +A+ K R FPGL GMDLA+EV+ +Y W+Q W Sbjct: 121 ILRDKGAQRGCVWAGVDVDPQVAVAKTRDFPGLKGMDLAREVSCRSSYVWSQTPWR---- 176 Query: 181 LPEAKKEDELP---FHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIF 237 P+ EL F VV YDFG K NILR+L GC +T+VPA A +VL++ PDG+ Sbjct: 177 -PDRSGYGELETPRFKVVVYDFGVKNNILRLLAGHGCEVTVVPATAPAAEVLRLAPDGVV 235 Query: 238 LSNGPGDPAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPV 297 LSNGPGDP PCDYAI AI+ L +PV GICLGHQLLALA GA+T KMKFGHHG NHPV Sbjct: 236 LSNGPGDPEPCDYAIEAIRILLAERMPVLGICLGHQLLALACGARTEKMKFGHHGANHPV 295 Query: 298 KDVEKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEAS 357 +++ VMI++QNHGF+V+EA+LPA+LR TH+SLFDG+LQGI T+ PA FQGHPEAS Sbjct: 296 QELATGRVMISSQNHGFSVEEASLPAHLRATHRSLFDGSLQGIEHTECPAIGFQGHPEAS 355 Query: 358 PGPHDAAPLFDHFIELI 374 PGP D LFD FIEL+ Sbjct: 356 PGPRDVETLFDRFIELM 372 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: 474 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_022949935.1 H035_RS0115815 (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.32647.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.5e-144 464.9 0.0 9.7e-144 464.7 0.0 1.0 1 lcl|NCBI__GCF_000421465.1:WP_022949935.1 H035_RS0115815 carbamoyl-phospha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000421465.1:WP_022949935.1 H035_RS0115815 carbamoyl-phosphate synthase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 464.7 0.0 9.7e-144 9.7e-144 1 360 [. 5 373 .. 5 374 .. 0.96 Alignments for each domain: == domain 1 score: 464.7 bits; conditional E-value: 9.7e-144 TIGR01368 1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaesk 69 a+l+ledGt f+g s+g ++ vGevvFnT++tGYqEiltDpsY++q+v+ltyp+ign+gvn+ed+es+ lcl|NCBI__GCF_000421465.1:WP_022949935.1 5 AILALEDGTLFQGVSIGGSGCRVGEVVFNTALTGYQEILTDPSYARQLVTLTYPHIGNVGVNPEDVESD 73 689****************************************************************** PP TIGR01368 70 kikvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkaviste.ksekee 137 i+++gl+v+++ +sn+r++esL+++lk++++v+i+++DTR+l++ lR+kg++++++ + +++ + lcl|NCBI__GCF_000421465.1:WP_022949935.1 74 YIHAAGLIVRDVPGVASNWRMTESLTAYLKRRDVVGIADIDTRKLTRILRDKGAQRGCVWAGvDVDPQV 142 **********************************************************98872556888 PP TIGR01368 138 lvekakespkvkevnlvkevstkeayeleq.....k....akkegkklrvvvidlGvKenilreLvkrg 197 +v+k+++ p +k+++l++evs+++ y ++q + + e+ + +vvv+d+GvK+nilr L+ +g lcl|NCBI__GCF_000421465.1:WP_022949935.1 143 AVAKTRDFPGLKGMDLAREVSCRSSYVWSQtpwrpDrsgyGELETPRFKVVVYDFGVKNNILRLLAGHG 211 99999************************9766651556567788889********************* PP TIGR01368 198 vevtvvpadtsaeeikklnpdgillsnGPGdPaaveeaietvkklleakiPifGIclGhqllalalgak 266 +evtvvpa+++a+e+ +l pdg++lsnGPGdP+ +++aie ++ ll +++P++GIclGhqllala ga+ lcl|NCBI__GCF_000421465.1:WP_022949935.1 212 CEVTVVPATAPAAEVLRLAPDGVVLSNGPGDPEPCDYAIEAIRILLAERMPVLGICLGHQLLALACGAR 280 ********************************************************************* PP TIGR01368 267 tyklkfGhrGaNhpvkdlktgrveitsqNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsv 335 t k+kfGh+GaNhpv++l+tgrv+i+sqNHg++v+e+sl+++ l++th++l+Dg+++g+eh+e p++ lcl|NCBI__GCF_000421465.1:WP_022949935.1 281 TEKMKFGHHGANHPVQELATGRVMISSQNHGFSVEEASLPAH-LRATHRSLFDGSLQGIEHTECPAIGF 348 **************************************8865.************************** PP TIGR01368 336 QyHPeaspGphdteylFdefvelik 360 Q HPeaspGp+d e+lFd+f+el++ lcl|NCBI__GCF_000421465.1:WP_022949935.1 349 QGHPEASPGPRDVETLFDRFIELMA 373 **********************996 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 9.92 // [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