Align Carbamoyl-phosphate synthase pyrimidine-specific small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate WP_027720987.1 H589_RS0104820 carbamoyl-phosphate synthase small subunit
Query= SwissProt::P25993 (364 letters) >NCBI__GCF_000425265.1:WP_027720987.1 Length = 374 Score = 327 bits (839), Expect = 2e-94 Identities = 165/376 (43%), Positives = 239/376 (63%), Gaps = 20/376 (5%) Query: 1 MKRRLVLENGAVFEGEAFGSLEHNMGEVVFNTGMTGYQEILSDPSYCGQIVTLTYPLIGN 60 MK L LE+G FEG +F + GE +FNTGMTGYQE+L+DPSY GQ+V +TYPLIGN Sbjct: 1 MKAILALEDGTWFEGTSFTGPGESGGEAIFNTGMTGYQEVLTDPSYTGQMVCMTYPLIGN 60 Query: 61 YGINRDDFESITPFVKGLIIKELCELPSNWRSAYTLDEYLKMKNIPGLQGIDTRKLTRMI 120 YG+ +D ES V I+KE C+ PSNWRS +L EYL+ I G++GIDTR LTR + Sbjct: 61 YGVTEEDLESAKIHVAAFIVKECCKNPSNWRSVMSLPEYLEKAGIMGIEGIDTRALTRHL 120 Query: 121 RTAGALKGTFASSDEDIEAVLKRLNE--TELPRNQVSQVSAKTAY------PSP------ 166 R GA++G ++ + D ++++ + T +N +V++ + Y P P Sbjct: 121 RINGAMRGIISTEELDPAKLVEKAKQLPTMEGQNLADKVTSDSCYAWIDNKPVPVDVSKG 180 Query: 167 ----GRGKRIVLVDFGMKHGILRELNKRKCDVIVVPYNITAEEVLQLKPDGIMLSNGPGD 222 G+G R+VLVD+G+K ILR L+ +V+ VP + T E++ L P+ I LSNGPGD Sbjct: 181 YEWTGKGPRLVLVDYGVKWNILRLLDAEGFEVLSVPSSYTEEQIRALNPEAIFLSNGPGD 240 Query: 223 PKDVPEAIEMIKGVLGKVPLFGICLGHQLFALACGANTEKMKFGHRGSNHPVKELATGKV 282 P + A++ K + +P+ GICLGHQ+ LA G + K+KFGH G NHPV ++ + K+ Sbjct: 241 PAVLDHAVKTAKSLCEDLPVAGICLGHQILGLALGGDAFKLKFGHHGCNHPVMDMESNKI 300 Query: 283 ALTSQNHGYTVSSISKTELEVTHIAINDDTIEGLKHKTLPAFTVQYHPEASPGPEDANHL 342 ++SQNHG+ V +L++TH +ND+T+EG HKT P +Q+HPEA+PGP D+ + Sbjct: 301 EISSQNHGFCVDISKCPDLKITHKNLNDETLEGFAHKTKPIIAIQFHPEAAPGPHDSCYF 360 Query: 343 FDRFIEMIETTEKEGE 358 F RF +M++ EK G+ Sbjct: 361 FARFRDMVK--EKTGK 374 Lambda K H 0.317 0.136 0.397 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: 404 Number of extensions: 12 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: 364 Length of database: 374 Length adjustment: 30 Effective length of query: 334 Effective length of database: 344 Effective search space: 114896 Effective search space used: 114896 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 (21.6 bits) S2: 49 (23.5 bits)
Align candidate WP_027720987.1 H589_RS0104820 (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.653.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.7e-145 468.5 0.0 7.7e-145 468.3 0.0 1.0 1 lcl|NCBI__GCF_000425265.1:WP_027720987.1 H589_RS0104820 carbamoyl-phospha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000425265.1:WP_027720987.1 H589_RS0104820 carbamoyl-phosphate synthase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 468.3 0.0 7.7e-145 7.7e-145 1 360 [. 3 369 .. 3 370 .. 0.97 Alignments for each domain: == domain 1 score: 468.3 bits; conditional E-value: 7.7e-145 TIGR01368 1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaesk 69 a+l+ledGt feg+sf ++e Ge +FnT+mtGYqE+ltDpsY+gq+v +typlignygv+eed es lcl|NCBI__GCF_000425265.1:WP_027720987.1 3 AILALEDGTWFEGTSFTGPGESGGEAIFNTGMTGYQEVLTDPSYTGQMVCMTYPLIGNYGVTEEDLESA 71 689****************************************************************** PP TIGR01368 70 kikvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavisteksekeel 138 ki+v++++vke++k++sn+r+ sL e+l++ gi++ieg+DTRal+++lR +g+m+++iste+ + +l lcl|NCBI__GCF_000425265.1:WP_027720987.1 72 KIHVAAFIVKECCKNPSNWRSVMSLPEYLEKAGIMGIEGIDTRALTRHLRINGAMRGIISTEELDPAKL 140 ********************************************************************* PP TIGR01368 139 vekakespkvkevnlvkevstkeayeleq......k....akkegkklrvvvidlGvKenilreLvkrg 197 vekak+ p+++++nl+++v+ ++ y++ + + + +gk r+v++d+GvK nilr L ++g lcl|NCBI__GCF_000425265.1:WP_027720987.1 141 VEKAKQLPTMEGQNLADKVTSDSCYAWIDnkpvpvDvskgYEWTGKGPRLVLVDYGVKWNILRLLDAEG 209 ****************************976666515556667777789******************** PP TIGR01368 198 vevtvvpadtsaeeikklnpdgillsnGPGdPaaveeaietvkklleakiPifGIclGhqllalalgak 266 +ev vp +++ e+i +lnp++i+lsnGPGdPa +++a++t k+l+e ++P+ GIclGhq+l+lalg++ lcl|NCBI__GCF_000425265.1:WP_027720987.1 210 FEVLSVPSSYTEEQIRALNPEAIFLSNGPGDPAVLDHAVKTAKSLCE-DLPVAGICLGHQILGLALGGD 277 ***********************************************.********************* PP TIGR01368 267 tyklkfGhrGaNhpvkdlktgrveitsqNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsv 335 +klkfGh+G Nhpv+d++++++ei+sqNHg+ vd + +l++th+nlnD+t+eg +hk++p++++ lcl|NCBI__GCF_000425265.1:WP_027720987.1 278 AFKLKFGHHGCNHPVMDMESNKIEISSQNHGFCVDISK--CPDLKITHKNLNDETLEGFAHKTKPIIAI 344 ************************************87..5589************************* PP TIGR01368 336 QyHPeaspGphdteylFdefvelik 360 Q+HPea+pGphd+ y+F +f +++k lcl|NCBI__GCF_000425265.1:WP_027720987.1 345 QFHPEAAPGPHDSCYFFARFRDMVK 369 *********************9997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (361 nodes) Target sequences: 1 (374 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: 7.81 // [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