Align Carbamoyl-phosphate synthase pyrimidine-specific small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate WP_017548471.1 C792_RS0105600 glutamine-hydrolyzing carbamoyl-phosphate synthase small subunit
Query= SwissProt::P25993 (364 letters) >NCBI__GCF_000330705.1:WP_017548471.1 Length = 363 Score = 397 bits (1020), Expect = e-115 Identities = 190/360 (52%), Positives = 256/360 (71%), Gaps = 3/360 (0%) Query: 2 KRRLVLENGAVFEGEAFGSLEHNMGEVVFNTGMTGYQEILSDPSYCGQIVTLTYPLIGNY 61 KR LVLE+G V+EG FGS GE+VFNT MTG QEI++D SY QI+T +YPLIGN Sbjct: 5 KRYLVLEDGTVYEGYRFGSDRTAEGELVFNTAMTGAQEIITDLSYTDQIITFSYPLIGNT 64 Query: 62 GINRDDFESITPFVKGLIIKELCELPSNWRSAYTLDEYLKMKNIPGLQGIDTRKLTRMIR 121 G+N +D E++ P +G++++E C PSN+R++ +LD +L+ NIPG+ G+DTR +TR IR Sbjct: 65 GVNIEDNETLVPSARGVVVREACSEPSNFRASESLDSFLRRHNIPGISGVDTRSITRKIR 124 Query: 122 TAGALKGTFASSDEDIEAVLKRLNETELPRNQVSQVSAKTAYPSPGRGKRIVLVDFGMKH 181 G +K + DE+ E ++ L +QV +VS + Y S G GKR+VLVD+G K Sbjct: 125 DKGVMKAVM-TDDENHEELVGLLQNASFRTDQVKRVSTRAPYISTGPGKRVVLVDYGKKE 183 Query: 182 GILRELNKRKCDVIVVPYNITAEEVLQLKPDGIMLSNGPGDPKDVPEAIEMIKGVLGKVP 241 I+R LN CDV VVP++ TAE++L++KPDG+MLSNGPGDP+DV I +K ++G+VP Sbjct: 184 NIVRSLNTHGCDVTVVPHDTTAEDILKMKPDGVMLSNGPGDPEDVEAGIRTVKNLIGRVP 243 Query: 242 LFGICLGHQLFALACGANTEKMKFGHRGSNHPVKELATGKVALTSQNHGYTV--SSISKT 299 LFGICLGHQL LACGA T KMKFGHRGSN PV ATG+V +T+QNHG+ + S+ T Sbjct: 244 LFGICLGHQLIGLACGAKTFKMKFGHRGSNQPVINHATGRVEITAQNHGFAIDADSLGST 303 Query: 300 ELEVTHIAINDDTIEGLKHKTLPAFTVQYHPEASPGPEDANHLFDRFIEMIETTEKEGEA 359 LE+TH A+ND T+EG++H P F+VQYHPEAS GP D+ +LF F+ M+ET ++ A Sbjct: 304 GLEITHTALNDRTVEGVRHVKHPVFSVQYHPEASAGPHDSEYLFGEFVNMMETKKEANNA 363 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: 399 Number of extensions: 16 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: 363 Length adjustment: 29 Effective length of query: 335 Effective length of database: 334 Effective search space: 111890 Effective search space used: 111890 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_017548471.1 C792_RS0105600 (glutamine-hydrolyzing 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.3412593.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.1e-150 485.3 0.1 5.9e-150 485.1 0.1 1.0 1 NCBI__GCF_000330705.1:WP_017548471.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000330705.1:WP_017548471.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 485.1 0.1 5.9e-150 5.9e-150 2 360 .. 7 355 .. 6 356 .. 0.96 Alignments for each domain: == domain 1 score: 485.1 bits; conditional E-value: 5.9e-150 TIGR01368 2 tlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskkikvk 74 +lvledGtv+eg+ fg+++++ Ge+vFnT+mtG qEi+tD sY++qi++++yplign+gvn ed+e + ++ NCBI__GCF_000330705.1:WP_017548471.1 7 YLVLEDGTVYEGYRFGSDRTAEGELVFNTAMTGAQEIITDLSYTDQIITFSYPLIGNTGVNIEDNETLVPSAR 79 8************************************************************************ PP TIGR01368 75 glvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavisteksekeelvekakespk 147 g+vv+e+++e+sn+ra+esL++fl++++i++i gvDTR++++k+R+kg+mkav+++++ ++eelv ++++ NCBI__GCF_000330705.1:WP_017548471.1 80 GVVVREACSEPSNFRASESLDSFLRRHNIPGISGVDTRSITRKIRDKGVMKAVMTDDE-NHEELVGLLQNASF 151 *****************************************************99998.66677775555544 PP TIGR01368 148 vkevnlvkevstkeayeleqkakkegkklrvvvidlGvKenilreLvkrgvevtvvpadtsaeeikklnpdgi 220 ++ vk+vst+ +y + g +rvv++d+G Keni+r+L ++g++vtvvp+dt+ae+i k++pdg+ NCBI__GCF_000330705.1:WP_017548471.1 152 R--TDQVKRVSTRAPYISTG----PG--KRVVLVDYGKKENIVRSLNTHGCDVTVVPHDTTAEDILKMKPDGV 216 4..699**********7773....44..46******************************************* PP TIGR01368 221 llsnGPGdPaaveeaietvkklleakiPifGIclGhqllalalgaktyklkfGhrGaNhpvkdlktgrveits 293 +lsnGPGdP++ve+ i+tvk+l++ ++P+fGIclGhql++la gakt+k+kfGhrG+N+pv++++tgrveit+ NCBI__GCF_000330705.1:WP_017548471.1 217 MLSNGPGDPEDVEAGIRTVKNLIG-RVPLFGICLGHQLIGLACGAKTFKMKFGHRGSNQPVINHATGRVEITA 288 ************************.************************************************ PP TIGR01368 294 qNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsvQyHPeaspGphdteylFdefvelik 360 qNHg+a+d +sl ++ le+th+ lnD tveg++h + pvfsvQyHPeas+Gphd+eylF efv++++ NCBI__GCF_000330705.1:WP_017548471.1 289 QNHGFAIDADSLGSTGLEITHTALNDRTVEGVRHVKHPVFSVQYHPEASAGPHDSEYLFGEFVNMME 355 ****************************************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (361 nodes) Target sequences: 1 (363 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 27.65 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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