Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate WP_041590260.1 TERTU_RS14580 carbamoyl-phosphate synthase small subunit
Query= SwissProt::P0A6F1 (382 letters) >NCBI__GCF_000023025.1:WP_041590260.1 Length = 407 Score = 550 bits (1416), Expect = e-161 Identities = 274/373 (73%), Positives = 308/373 (82%), Gaps = 6/373 (1%) Query: 5 ALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNVG 64 A+LVLEDG+ F G +IGATG +VGEVVFNTS+TGYQEILTDPSY+RQIVTLTYPHIGN G Sbjct: 34 AILVLEDGSVFRGVSIGATGKSVGEVVFNTSITGYQEILTDPSYARQIVTLTYPHIGNTG 93 Query: 65 TNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTRLLRE 124 TN DEE + A GLVIRDLPL+ASNFRN++ L YL NI+ IADIDTR+LTRLLR+ Sbjct: 94 TNSEDEECKTIWATGLVIRDLPLLASNFRNSQSLDQYLSSKNILGIADIDTRRLTRLLRD 153 Query: 125 KGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGGL-PE 183 KGA GCI+AGD D A ALE AR F GL GMDLAKEV+T + Y W GSW L G P Sbjct: 154 KGALAGCIMAGD-VDEAEALETARGFAGLQGMDLAKEVSTKDTYQWRDGSWKLGSGYAPL 212 Query: 184 AKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSNGPG 243 A+K F+VVAYD+GAK NILRMLVDRGC LT+VPAQT A DVL MNPDG+FLSNGPG Sbjct: 213 AEKR----FNVVAYDYGAKSNILRMLVDRGCDLTVVPAQTPAADVLAMNPDGVFLSNGPG 268 Query: 244 DPAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDVEKN 303 DP PCDYAI AI+ L ++P+FGICLGHQLLALASGAKT+KMKFGHHGGNHPV++V+ Sbjct: 269 DPEPCDYAIDAIKVLLNENMPIFGICLGHQLLALASGAKTIKMKFGHHGGNHPVQNVKTG 328 Query: 304 VVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGPHDA 363 VMIT+QNHGFA DE+TLP L THKSLFDG+LQGIHRTDKPAFSFQGHPEASPGPHDA Sbjct: 329 EVMITSQNHGFAADESTLPDCLEATHKSLFDGSLQGIHRTDKPAFSFQGHPEASPGPHDA 388 Query: 364 APLFDHFIELIEQ 376 A LFDHFIEL++Q Sbjct: 389 AELFDHFIELMQQ 401 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: 525 Number of extensions: 18 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: 407 Length adjustment: 31 Effective length of query: 351 Effective length of database: 376 Effective search space: 131976 Effective search space used: 131976 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_041590260.1 TERTU_RS14580 (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.810.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-151 490.5 0.0 1.6e-151 490.3 0.0 1.0 1 lcl|NCBI__GCF_000023025.1:WP_041590260.1 TERTU_RS14580 carbamoyl-phosphat Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000023025.1:WP_041590260.1 TERTU_RS14580 carbamoyl-phosphate synthase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 490.3 0.0 1.6e-151 1.6e-151 1 360 [. 34 400 .. 34 401 .. 0.97 Alignments for each domain: == domain 1 score: 490.3 bits; conditional E-value: 1.6e-151 TIGR01368 1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaesk 69 a+lvledG+vf+g s+ga+++ vGevvFnTs+tGYqEiltDpsY++qiv+ltyp+ign+g+n+ed+e k lcl|NCBI__GCF_000023025.1:WP_041590260.1 34 AILVLEDGSVFRGVSIGATGKSVGEVVFNTSITGYQEILTDPSYARQIVTLTYPHIGNTGTNSEDEECK 102 68******************************************************************* PP TIGR01368 70 kikvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavisteksekeel 138 +i+++glv+++l +sn+r+++sL+++l++++i +i+++DTR l++ lR+kg+++++i++ ++++ e+ lcl|NCBI__GCF_000023025.1:WP_041590260.1 103 TIWATGLVIRDLPLLASNFRNSQSLDQYLSSKNILGIADIDTRRLTRLLRDKGALAGCIMAGDVDEAEA 171 ********************************************************************* PP TIGR01368 139 vekakespkvkevnlvkevstkeayeleq...k.....akkegkklrvvvidlGvKenilreLvkrgve 199 e+a+ + +++++l+kevstk++y++++ k a +k+ +vv++d+G K+nilr+Lv+rg++ lcl|NCBI__GCF_000023025.1:WP_041590260.1 172 LETARGFAGLQGMDLAKEVSTKDTYQWRDgswKlgsgyAPLAEKRFNVVAYDYGAKSNILRMLVDRGCD 240 ****************************977715556577788889*********************** PP TIGR01368 200 vtvvpadtsaeeikklnpdgillsnGPGdPaaveeaietvkklleakiPifGIclGhqllalalgakty 268 +tvvpa+t+a+++ ++npdg++lsnGPGdP+ +++ai+ +k ll++++PifGIclGhqllala+gakt+ lcl|NCBI__GCF_000023025.1:WP_041590260.1 241 LTVVPAQTPAADVLAMNPDGVFLSNGPGDPEPCDYAIDAIKVLLNENMPIFGICLGHQLLALASGAKTI 309 ********************************************************************* PP TIGR01368 269 klkfGhrGaNhpvkdlktgrveitsqNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsvQy 337 k+kfGh+G+Nhpv+++ktg+v+itsqNHg+a de++l+ + le+th++l+Dg+++g++++++p+fs Q lcl|NCBI__GCF_000023025.1:WP_041590260.1 310 KMKFGHHGGNHPVQNVKTGEVMITSQNHGFAADESTLP-DCLEATHKSLFDGSLQGIHRTDKPAFSFQG 377 **********************************9977.67**************************** PP TIGR01368 338 HPeaspGphdteylFdefvelik 360 HPeaspGphd++ lFd+f+el++ lcl|NCBI__GCF_000023025.1:WP_041590260.1 378 HPEASPGPHDAAELFDHFIELMQ 400 *********************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (361 nodes) Target sequences: 1 (407 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: 12.23 // [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