Align Carbamoyl-phosphate synthase pyrimidine-specific small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate WP_048102833.1 MBAR_RS12625 carbamoyl-phosphate synthase small subunit
Query= SwissProt::P25993 (364 letters) >NCBI__GCF_000195895.1:WP_048102833.1 Length = 368 Score = 290 bits (742), Expect = 4e-83 Identities = 151/356 (42%), Positives = 217/356 (60%), Gaps = 13/356 (3%) Query: 1 MKRRLVLENGAVFEGEAFGSLEHNMGEVVFNTGMTGYQEILSDPSYCGQIVTLTYPLIGN 60 MK L LE+G V +G FG+ GE+VF T TGY+E L+DPSY GQI+ TYPLIGN Sbjct: 1 MKAVLGLEDGTVIKGTGFGAEGTACGELVFTTQFTGYEEALTDPSYKGQILMFTYPLIGN 60 Query: 61 YGINRDDFESITPFVKGLIIKELCELPSNWRSAYTLDEYLKMKNIPGLQGIDTRKLTRMI 120 YG++ + +S +GL+++E C+ P +++S+ +++++L+ + PG++G+DTR LT Sbjct: 61 YGVSGERVQSDNMHAEGLVVREACKKPYHYKSSRSINKFLEDEGKPGIEGVDTRMLTIRA 120 Query: 121 RTAGALKGTF-ASSDEDIEAVLKRLNETELPRNQ-VSQVSAKTAYPSPG---------RG 169 R G ++ A SD+ EAV N +L + +S V+ K Y PG + Sbjct: 121 REHGTMRAALIAGSDDGEEAVDVARNAPQLTDEELISLVTCKEPYFIPGAEGAWKGGSKR 180 Query: 170 KRIVLVDFGMKHGILRELNKRKCDVIVVPYNITAEEVLQLKPDGIMLSNGPGDPKDVPEA 229 K V+VD G+K I+ L+KR D+ +VP E+ +PD + +SNGPGDP+ +A Sbjct: 181 KHAVIVDLGIKRNIINNLHKRGIDLTLVPATTKPSEIANYEPDLLFISNGPGDPEKATDA 240 Query: 230 IEMIKGVLGKVPLFGICLGHQLFALACGANTEKMKFGHRGSNHPVKELATGKVALTSQNH 289 I +K G +P+ GIC GHQ+ +LA GA T K+KFGHRG N PVK+L K+ +TSQNH Sbjct: 241 INAVKAFAGTIPVCGICFGHQIISLAMGAKTYKLKFGHRGGNQPVKDLIENKIFITSQNH 300 Query: 290 GYTV--SSISKTELEVTHIAINDDTIEGLKHKTLPAFTVQYHPEASPGPEDANHLF 343 GY V S+ T L V ++ ND T+EG+ HK L F+VQ+HPEA GP D F Sbjct: 301 GYAVDADSLDGTGLYVKYLNANDKTVEGVSHKDLDVFSVQFHPEAQAGPMDTEETF 356 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: 374 Number of extensions: 15 Number of successful extensions: 3 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: 368 Length adjustment: 30 Effective length of query: 334 Effective length of database: 338 Effective search space: 112892 Effective search space used: 112892 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_048102833.1 MBAR_RS12625 (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.26611.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.5e-142 458.1 0.0 1.1e-141 457.9 0.0 1.0 1 lcl|NCBI__GCF_000195895.1:WP_048102833.1 MBAR_RS12625 carbamoyl-phosphate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000195895.1:WP_048102833.1 MBAR_RS12625 carbamoyl-phosphate synthase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 457.9 0.0 1.1e-141 1.1e-141 1 356 [. 3 361 .. 3 365 .. 0.96 Alignments for each domain: == domain 1 score: 457.9 bits; conditional E-value: 1.1e-141 TIGR01368 1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaesk 69 a+l ledGtv++g++fgae++++Ge+vF+T +tGY+E+ltDpsYkgqi+++typlignygv e ++s+ lcl|NCBI__GCF_000195895.1:WP_048102833.1 3 AVLGLEDGTVIKGTGFGAEGTACGELVFTTQFTGYEEALTDPSYKGQILMFTYPLIGNYGVSGERVQSD 71 5789***************************************************************** PP TIGR01368 70 kikvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavisteksekeel 138 +++++glvv+e++k++ +y++++s+++fl++eg ++iegvDTR+l+ + Re+g+m+a++ + + + ee+ lcl|NCBI__GCF_000195895.1:WP_048102833.1 72 NMHAEGLVVREACKKPYHYKSSRSINKFLEDEGKPGIEGVDTRMLTIRAREHGTMRAALIAGSDDGEEA 140 ********************************************************************* PP TIGR01368 139 vekakespkvkevnlvkevstkeayeleqk...akkegkklrvvvidlGvKenilreLvkrgvevtvvp 204 v+ a+++p++++ +l++ v++ke+y + k +k+++ v++dlG+K+ni+++L krg+++t+vp lcl|NCBI__GCF_000195895.1:WP_048102833.1 141 VDVARNAPQLTDEELISLVTCKEPYFIPGAegaWKGGSKRKHAVIVDLGIKRNIINNLHKRGIDLTLVP 209 *************************999833534444555899************************** PP TIGR01368 205 adtsaeeikklnpdgillsnGPGdPaaveeaietvkklleakiPifGIclGhqllalalgaktyklkfG 273 a+t+ +ei++++pd +++snGPGdP+++++ai+ vk++++ +iP+ GIc+Ghq+++la+gaktyklkfG lcl|NCBI__GCF_000195895.1:WP_048102833.1 210 ATTKPSEIANYEPDLLFISNGPGDPEKATDAINAVKAFAG-TIPVCGICFGHQIISLAMGAKTYKLKFG 277 ****************************************.**************************** PP TIGR01368 274 hrGaNhpvkdlktgrveitsqNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsvQyHPeas 342 hrG+N+pvkdl++++++itsqNHgyavd +sl+ + l v+ n nD+tveg++hk+l vfsvQ+HPea+ lcl|NCBI__GCF_000195895.1:WP_048102833.1 278 HRGGNQPVKDLIENKIFITSQNHGYAVDADSLDGTGLYVKYLNANDKTVEGVSHKDLDVFSVQFHPEAQ 346 ********************************************************************* PP TIGR01368 343 pGphdtey.lFdefv 356 +Gp dte +F ++v lcl|NCBI__GCF_000195895.1:WP_048102833.1 347 AGPMDTEEtFFGKVV 361 ******861555555 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (361 nodes) Target sequences: 1 (368 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: 7.96 // [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