Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate H281DRAFT_04402 H281DRAFT_04402 carbamoyl-phosphate synthase small subunit
Query= SwissProt::P0A6F1 (382 letters) >FitnessBrowser__Burk376:H281DRAFT_04402 Length = 384 Score = 496 bits (1276), Expect = e-145 Identities = 243/371 (65%), Positives = 289/371 (77%), Gaps = 4/371 (1%) Query: 5 ALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNVG 64 ALL L DGT F G +IGA G +GEVVFNT++TGYQEILTDPSY+RQIVTLTYPHIGNVG Sbjct: 8 ALLALADGTVFRGYSIGAPGHTIGEVVFNTAITGYQEILTDPSYARQIVTLTYPHIGNVG 67 Query: 65 TNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTRLLRE 124 N D E+++VHA GL+IRDLP++ASNFR L+ YL+ +VAIA +DTRKLTR+LR+ Sbjct: 68 VNAEDVEATKVHAAGLIIRDLPVLASNFRMERTLTQYLQDEGVVAIAGLDTRKLTRVLRD 127 Query: 125 KGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGGLPEA 184 KGAQNG I+AG + D A A+E AR+FPGL GMDLAK V+T E Y WTQ W L G Sbjct: 128 KGAQNGAILAGSD-DEAKAIELARSFPGLAGMDLAKVVSTKETYEWTQTEWRLESGYG-- 184 Query: 185 KKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSNGPGD 244 K++ + VVA+D+G K NILRML +RGC +T++PA+ SA D L +NPDGIFLSNGPGD Sbjct: 185 -KQNAPKYRVVAFDYGVKYNILRMLAERGCHVTVLPAEASAADALALNPDGIFLSNGPGD 243 Query: 245 PAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDVEKNV 304 P PCDYAI A ++ +E IP FGICLGHQ++ LA GA+TVKMK GHHG NHPVKD++ Sbjct: 244 PEPCDYAIAATKELIERGIPTFGICLGHQIMGLALGARTVKMKTGHHGANHPVKDLDDGR 303 Query: 305 VMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGPHDAA 364 V+IT+QNHGFAVD TLPAN RVTH SLFDGTLQG +DKPAF FQGHPEASPGPHD A Sbjct: 304 VIITSQNHGFAVDADTLPANARVTHVSLFDGTLQGFALSDKPAFCFQGHPEASPGPHDIA 363 Query: 365 PLFDHFIELIE 375 LFD F L++ Sbjct: 364 YLFDRFTALMD 374 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: 518 Number of extensions: 17 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: 382 Length of database: 384 Length adjustment: 30 Effective length of query: 352 Effective length of database: 354 Effective search space: 124608 Effective search space used: 124608 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 H281DRAFT_04402 H281DRAFT_04402 (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.7322.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-147 477.2 0.0 1.7e-147 477.0 0.0 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_04402 H281DRAFT_04402 carbamoyl-phosph Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_04402 H281DRAFT_04402 carbamoyl-phosphate synthase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 477.0 0.0 1.7e-147 1.7e-147 1 360 [. 8 374 .. 8 375 .. 0.97 Alignments for each domain: == domain 1 score: 477.0 bits; conditional E-value: 1.7e-147 TIGR01368 1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneeda 66 a l+l+dGtvf+g+s+ga+++++GevvFnT++tGYqEiltDpsY++qiv+ltyp+ign+gvn+ed+ lcl|FitnessBrowser__Burk376:H281DRAFT_04402 8 ALLALADGTVFRGYSIGAPGHTIGEVVFNTAITGYQEILTDPSYARQIVTLTYPHIGNVGVNAEDV 73 579*************************************************************** PP TIGR01368 67 eskkikvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavistek 132 e++k++++gl++++l +sn+r++++L+++l++eg+vai+g+DTR+l++ lR+kg+++++i + + lcl|FitnessBrowser__Burk376:H281DRAFT_04402 74 EATKVHAAGLIIRDLPVLASNFRMERTLTQYLQDEGVVAIAGLDTRKLTRVLRDKGAQNGAILAGS 139 ****************************************************************** PP TIGR01368 133 sekeelvekakespkvkevnlvkevstkeayeleq.....k...akkegkklrvvvidlGvKenil 190 ++ +++e a++ p +++++l+k vstke+ye++q + k++ k+rvv++d+GvK nil lcl|FitnessBrowser__Burk376:H281DRAFT_04402 140 DDEAKAIELARSFPGLAGMDLAKVVSTKETYEWTQtewrlEsgyGKQNAPKYRVVAFDYGVKYNIL 205 **********************************976655166677888889************** PP TIGR01368 191 reLvkrgvevtvvpadtsaeeikklnpdgillsnGPGdPaaveeaietvkklleakiPifGIclGh 256 r+L++rg++vtv+pa++sa++ +lnpdgi+lsnGPGdP+ +++ai+ +k+l+e+ iP+fGIclGh lcl|FitnessBrowser__Burk376:H281DRAFT_04402 206 RMLAERGCHVTVLPAEASAADALALNPDGIFLSNGPGDPEPCDYAIAATKELIERGIPTFGICLGH 271 ****************************************************************** PP TIGR01368 257 qllalalgaktyklkfGhrGaNhpvkdlktgrveitsqNHgyavdeeslkeeelevthvnlnDgtv 322 q+++lalga+t+k+k Gh+GaNhpvkdl++grv itsqNHg+avd ++l+++ ++vthv+l+Dgt+ lcl|FitnessBrowser__Burk376:H281DRAFT_04402 272 QIMGLALGARTVKMKTGHHGANHPVKDLDDGRVIITSQNHGFAVDADTLPAN-ARVTHVSLFDGTL 336 ************************************************8866.9************ PP TIGR01368 323 eglehkelpvfsvQyHPeaspGphdteylFdefvelik 360 +g + +++p+f Q HPeaspGphd +ylFd+f+ l++ lcl|FitnessBrowser__Burk376:H281DRAFT_04402 337 QGFALSDKPAFCFQGHPEASPGPHDIAYLFDRFTALMD 374 **********************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (361 nodes) Target sequences: 1 (384 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 9.31 // [ok]
This GapMind analysis is from Apr 09 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