Align Carbamoyl-phosphate synthase large chain, chloroplastic; Carbamoyl-phosphate synthetase ammonia chain; Protein VENOSA 3; EC 6.3.5.5 (characterized)
to candidate WP_013538311.1 THEAM_RS07915 carbamoyl-phosphate synthase large subunit
Query= SwissProt::Q42601
(1187 letters)
>NCBI__GCF_000185805.1:WP_013538311.1
Length = 1073
Score = 1263 bits (3267), Expect = 0.0
Identities = 651/1089 (59%), Positives = 827/1089 (75%), Gaps = 26/1089 (2%)
Query: 94 KRTDLKKIMILGAGPIVIGQACEFDYSGTQACKALREEGYEVILINSNPATIMTDPETAN 153
KRTDL+KI+I+G+GPIVIGQA EFDYSGTQACKAL+EEGY+V+L+NSNPATIMTDP+ A+
Sbjct: 3 KRTDLRKILIIGSGPIVIGQAAEFDYSGTQACKALKEEGYQVVLVNSNPATIMTDPDIAD 62
Query: 154 RTYIAPMTPELVEQVIEKERPDALLPTMGGQTALNLAVALAESGALEKYGVELIGAKLGA 213
RTYI P+T E++E++IEKERPDALLPT+GGQTALNLAV L E+G LEKYGVELIGAK+ A
Sbjct: 63 RTYIEPLTVEVLEKIIEKERPDALLPTVGGQTALNLAVKLHEAGILEKYGVELIGAKVEA 122
Query: 214 IKKAEDRELFKDAMKNIGLKTPPSGIGTTLDECFDIAEKIGEFPLIIRPAFTLGGTGGGI 273
IKKAEDRELFK+AM IGL+ P SG TL+E ++ +++G P IIRPAFTLGG GGG+
Sbjct: 123 IKKAEDRELFKEAMLKIGLEVPKSGTAHTLEEALEVVKEVG-LPAIIRPAFTLGGEGGGV 181
Query: 274 AYNKEEFESICKSGLAASATSQVLVEKSLLGWKEYELEVMRDLADNVVIICSIENIDPMG 333
AYN EEF+ I K GLAAS S++L+E+S+LGWKEYELEVMRDL DNVVIICSIEN+DPMG
Sbjct: 182 AYNIEEFKEIAKKGLAASPVSEILIEESVLGWKEYELEVMRDLNDNVVIICSIENVDPMG 241
Query: 334 VHTGDSITVAPAQTLTDREYQRLRDYSIAIIREIGVECGGSNVQFAVNPVDGEVMIIEMN 393
VHTGDSITVAPAQTLTD+EYQ LRD +IAIIREIGVE GGSNVQFAVNP +G V++IEMN
Sbjct: 242 VHTGDSITVAPAQTLTDKEYQVLRDAAIAIIREIGVETGGSNVQFAVNPENGRVIVIEMN 301
Query: 394 PRVSRSSALASKATGFPIAKMAAKLSVGYTLDQIPNDITRKTPASFEPSIDYVVTKIPRF 453
PRVSRSSALASKATGFPIAK+AAKL+VGYTLD++PNDIT+KTPASFEP+IDY V K PR+
Sbjct: 302 PRVSRSSALASKATGFPIAKIAAKLAVGYTLDELPNDITKKTPASFEPAIDYCVVKFPRW 361
Query: 454 AFEKFPGSQPLLTTQMKSVGESMALGRTFQESFQKALRSLECGFSGWGCAKIKELDWDWD 513
AFEKFP + LTT+MKSVGE MA+GRTF+E+ KA+RSLE G G ++ L
Sbjct: 362 AFEKFPEADSTLTTRMKSVGEVMAIGRTFKEALLKAVRSLEIGRYGLTMKGVERL--SDS 419
Query: 514 QLKYSLRVPNPDRIHAIYAAMKKGMKIDEIYELSMVDKWFLTQLKELVDVEQYLMSGTLS 573
+L+ + VPN DRI I A ++G ++++YELS +D+WFL +++LV++E L T+
Sbjct: 420 ELESRIAVPNADRIWYIAEAFRRGWSLEKLYELSRIDRWFLHNIRQLVELEGELKKHTVD 479
Query: 574 EITKEDLYEVKKRGFSDKQIAFATKTTEEEVRTKRISLGVVPSYKRVDTCAAEFEAHTPY 633
+ E L KK GFSD++IA TTE+ VR KR SL V YK VDTCA EFEA+TPY
Sbjct: 480 TVPGELLKWAKKWGFSDREIASLLGTTEKAVREKRKSLAPV-LYKTVDTCAGEFEAYTPY 538
Query: 634 MYSSYD-VECESAPNNKKKVLILGGGPNRIGQGIEFDYCCCHTSFALQDAGYETIMLNSN 692
YS+YD ECE+ P+ K+KV + G GPNRIGQG+EFDYCC H +AL++ GYE M+N N
Sbjct: 539 YYSTYDGRECEANPSKKEKVTVFGSGPNRIGQGVEFDYCCVHAVWALRELGYEAHMVNCN 598
Query: 693 PETVSTDYDTSDRLYFEPLTIEDVLNVIDLEKPDGIIVQFGGQTPLKLALPIKHYLDKHM 752
PETVSTDYDTSD+L+FEPLT+ED LNV++ EKP G++VQFGGQTPLKL++P++
Sbjct: 599 PETVSTDYDTSDKLFFEPLTLEDALNVVEKEKPLGVVVQFGGQTPLKLSVPLER------ 652
Query: 753 PMSLSGAGPVRIWGTSPDSIDAAEDRERFNAILDELKIEQPKGGIAKSEADALAIAKEVG 812
V+I GTS +SID AEDRERF +L+ L ++QP GIA+S +A IA+E+G
Sbjct: 653 -------EGVKILGTSSESIDIAEDRERFRELLNRLGLKQPPSGIARSLEEAEKIAQEIG 705
Query: 813 YPVVVRPSYVLGGRAMEIVYDDSRLITYLENAVQVDPERPVLVDKYLSDAIEIDVDTLTD 872
+PV++RPSYVLGGRAM IVY L Y+ AV+V E+PVL+DK+L DA+E DVD + D
Sbjct: 706 FPVLMRPSYVLGGRAMRIVYSMEELRQYMAEAVEVSEEKPVLIDKFLEDAVEFDVDAVAD 765
Query: 873 SYGNVVIGGIMEHIEQAGVHSGDSACMLPTQTIPASCLQTIRTWTTKLAKKLNVCGLMNC 932
VVIGG+MEHIE+AG+HSGDSAC+LPT ++ ++ I+ T K+A +LNV GL+N
Sbjct: 766 G-EEVVIGGVMEHIEEAGIHSGDSACVLPTFSVSRDIVEKIKEITRKIALELNVKGLINI 824
Query: 933 QYAITTSGDVFLLEANPRASRTVPFVSKAIGHPLAKYAALVMSGKSLKDLNFEKEVIPKH 992
Q+A+ G+++++E NPRASRTVPFVSKA G PLAK A V GK L++L KEV P++
Sbjct: 825 QFAV-KDGEIYIIEVNPRASRTVPFVSKATGIPLAKVATKVAMGKKLRELGV-KEVEPEY 882
Query: 993 VSVKEAVFPFEKFQGCDVILGPEMRSTGEVMSISSEFSSAFAMAQIAAGQKLPLS---GT 1049
SVKEAVFPF +F D +LGPEM+STGEVM I + AF AQ+AAG +LPL G
Sbjct: 883 YSVKEAVFPFNRFPEVDPVLGPEMKSTGEVMGIDPDVGIAFYKAQLAAGSRLPLDPSCGK 942
Query: 1050 VFLSLNDMTKPHLEKIAVSFLELGFKIVATSGTAHFLELKGIPVERVLKLHEG-RPHAAD 1108
VF+S+ D KP + +A ++GFKIV+T GT FL KGIPVE V KL EG RP+ D
Sbjct: 943 VFISVKDKDKPKIYSVAKQLADMGFKIVSTEGTYRFLREKGIPVELVYKLQEGRRPNIGD 1002
Query: 1109 MVANGQIHLMLITSSGDALDQKDGRQLRQMALAYKVPVITTVAGALATAEGIKSLKSSAI 1168
++ NG++ L++ T +G ++D +R++A+ Y +P TTV GA I +++ ++
Sbjct: 1003 LIKNGEVCLIINTPTG-TRSKRDAYSIRRLAVNYGIPYYTTVRGAEMAVRAISAMRKGSL 1061
Query: 1169 KMTALQDFF 1177
+ LQD++
Sbjct: 1062 NVKPLQDYY 1070
Lambda K H
0.317 0.133 0.383
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: 3174
Number of extensions: 134
Number of successful extensions: 22
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: 1187
Length of database: 1073
Length adjustment: 46
Effective length of query: 1141
Effective length of database: 1027
Effective search space: 1171807
Effective search space used: 1171807
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: 58 (26.9 bits)
Align candidate WP_013538311.1 THEAM_RS07915 (carbamoyl-phosphate synthase large subunit)
to HMM TIGR01369 (carB: carbamoyl-phosphate synthase, large 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/TIGR01369.hmm
# target sequence database: /tmp/gapView.6777.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR01369 [M=1052]
Accession: TIGR01369
Description: CPSaseII_lrg: carbamoyl-phosphate synthase, large 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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
0 1607.0 0.0 0 1606.8 0.0 1.0 1 lcl|NCBI__GCF_000185805.1:WP_013538311.1 THEAM_RS07915 carbamoyl-phosphat
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000185805.1:WP_013538311.1 THEAM_RS07915 carbamoyl-phosphate synthase large subunit
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1606.8 0.0 0 0 1 1051 [. 2 1052 .. 2 1053 .. 0.99
Alignments for each domain:
== domain 1 score: 1606.8 bits; conditional E-value: 0
TIGR01369 1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYieP 67
pkr+d++k+l+iGsGpivigqAaEFDYsG+qa+kalkeeg++vvLvnsn+At+mtd+++ad++YieP
lcl|NCBI__GCF_000185805.1:WP_013538311.1 2 PKRTDLRKILIIGSGPIVIGQAAEFDYSGTQACKALKEEGYQVVLVNSNPATIMTDPDIADRTYIEP 68
689**************************************************************** PP
TIGR01369 68 ltveavekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkea 134
ltve++ekiiekErpDa+l+t+GGqtaLnlav+l+e+G+Lekygv+l+G+kveaikkaedRe+Fkea
lcl|NCBI__GCF_000185805.1:WP_013538311.1 69 LTVEVLEKIIEKERPDALLPTVGGQTALNLAVKLHEAGILEKYGVELIGAKVEAIKKAEDRELFKEA 135
******************************************************************* PP
TIGR01369 135 lkeineevakseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspik 201
+ +i++ev+ks ++++ eeale+++e+g+P i+R+aftlgG+G+g+a+n ee+ke+++k+l+asp++
lcl|NCBI__GCF_000185805.1:WP_013538311.1 136 MLKIGLEVPKSGTAHTLEEALEVVKEVGLPAIIRPAFTLGGEGGGVAYNIEEFKEIAKKGLAASPVS 202
******************************************************************* PP
TIGR01369 202 qvlvekslagwkEiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdasl 268
++l+e+s+ gwkE+E+Ev+RD +dn++i+c+iEn+Dp+GvHtGdsi+vaP+qtLtdkeyq lRda++
lcl|NCBI__GCF_000185805.1:WP_013538311.1 203 EILIEESVLGWKEYELEVMRDLNDNVVIICSIENVDPMGVHTGDSITVAPAQTLTDKEYQVLRDAAI 269
******************************************************************* PP
TIGR01369 269 kiirelgvege.cnvqfaldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelk 334
+iire+gve++ +nvqfa++Pe+ r++viE+npRvsRssALAskAtG+PiAk+aaklavGy+Ldel+
lcl|NCBI__GCF_000185805.1:WP_013538311.1 270 AIIREIGVETGgSNVQFAVNPENGRVIVIEMNPRVSRSSALASKATGFPIAKIAAKLAVGYTLDELP 336
*********988******************************************************* PP
TIGR01369 335 ndvtketvAsfEPslDYvvvkiPrwdldkfekvdrklgtqmksvGEvmaigrtfeealqkalrslee 401
nd+tk+t+AsfEP++DY+vvk+Prw+++kf ++d++l+t+mksvGEvmaigrtf+eal+ka+rsle+
lcl|NCBI__GCF_000185805.1:WP_013538311.1 337 NDITKKTPASFEPAIDYCVVKFPRWAFEKFPEADSTLTTRMKSVGEVMAIGRTFKEALLKAVRSLEI 403
******************************************************************* PP
TIGR01369 402 kllglklkekeaesdeeleealkkpndrRlfaiaealrrgvsveevyeltkidrffleklkklvele 468
+ +gl++k e sd+ele+++ pn++R+++iaea+rrg s+e++yel++idr+fl+++++lvele
lcl|NCBI__GCF_000185805.1:WP_013538311.1 404 GRYGLTMKGVERLSDSELESRIAVPNADRIWYIAEAFRRGWSLEKLYELSRIDRWFLHNIRQLVELE 470
******************************************************************* PP
TIGR01369 469 keleeeklkelkkellkkakklGfsdeqiaklvkvseaevrklrkelgivpvvkrvDtvaaEfeakt 535
el++++++ ++ ellk akk Gfsd++ia+l++++e++vr+ rk+l ++k+vDt+a+Efea t
lcl|NCBI__GCF_000185805.1:WP_013538311.1 471 GELKKHTVDTVPGELLKWAKKWGFSDREIASLLGTTEKAVREKRKSLA-PVLYKTVDTCAGEFEAYT 536
********************************************9875.4579************** PP
TIGR01369 536 pYlYstyeeekddvevtekkkvlvlGsGpiRigqgvEFDycavhavlalreagyktilinynPEtvs 602
pY+Ysty + + +++ ++k+kv v GsGp+RigqgvEFDyc+vhav+alre gy++ ++n+nPEtvs
lcl|NCBI__GCF_000185805.1:WP_013538311.1 537 PYYYSTYDGRECEANPSKKEKVTVFGSGPNRIGQGVEFDYCCVHAVWALRELGYEAHMVNCNPETVS 603
**********999999999************************************************ PP
TIGR01369 603 tDydiadrLyFeeltvedvldiiekekvegvivqlgGqtalnlakeleeagvkilGtsaesidraEd 669
tDyd++d+L+Fe+lt+ed l+++ekek+ gv+vq+gGqt+l+l+ le++gvkilGts esid+aEd
lcl|NCBI__GCF_000185805.1:WP_013538311.1 604 TDYDTSDKLFFEPLTLEDALNVVEKEKPLGVVVQFGGQTPLKLSVPLEREGVKILGTSSESIDIAED 670
******************************************************************* PP
TIGR01369 670 RekFsklldelgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgGrameiveneeeleryleea 736
Re+F +ll++lg+kqp +a+s+eea++ia+eig+Pvl+RpsyvlgGram+iv+++eel++y+ ea
lcl|NCBI__GCF_000185805.1:WP_013538311.1 671 RERFRELLNRLGLKQPPSGIARSLEEAEKIAQEIGFPVLMRPSYVLGGRAMRIVYSMEELRQYMAEA 737
******************************************************************* PP
TIGR01369 737 vevskekPvlidkyledavEvdvDavadgeevliagileHiEeaGvHsGDstlvlppqklseevkkk 803
vevs+ekPvlidk+ledavE+dvDavadgeev+i g++eHiEeaG+HsGDs++vlp+ ++s+++++k
lcl|NCBI__GCF_000185805.1:WP_013538311.1 738 VEVSEEKPVLIDKFLEDAVEFDVDAVADGEEVVIGGVMEHIEEAGIHSGDSACVLPTFSVSRDIVEK 804
******************************************************************* PP
TIGR01369 804 ikeivkkiakelkvkGllniqfvvkdeevyviEvnvRasRtvPfvskalgvplvklavkvllgkkle 870
ikei++kia el+vkGl+niqf+vkd+e+y+iEvn+RasRtvPfvska+g+pl+k+a+kv +gkkl+
lcl|NCBI__GCF_000185805.1:WP_013538311.1 805 IKEITRKIALELNVKGLINIQFAVKDGEIYIIEVNPRASRTVPFVSKATGIPLAKVATKVAMGKKLR 871
******************************************************************* PP
TIGR01369 871 elekgvkkekksklvavkaavfsfsklagvdvvlgpemkstGEvmgigrdleeallkallaskakik 937
el+ ke ++++++vk+avf+f+++ +vd+vlgpemkstGEvmgi+ d+ a++ka+la++++++
lcl|NCBI__GCF_000185805.1:WP_013538311.1 872 ELGV---KEVEPEYYSVKEAVFPFNRFPEVDPVLGPEMKSTGEVMGIDPDVGIAFYKAQLAAGSRLP 935
*876...9999****************************************************8887 PP
TIGR01369 938 kk...gsvllsvkdkdkeellelakklaekglkvyategtakvleeagikaevvlkvseea.ekile 1000
+ g+v++svkdkdk ++ ++ak+la++g+k+++tegt ++l+e+gi +e+v+k +e + ++i +
lcl|NCBI__GCF_000185805.1:WP_013538311.1 936 LDpscGKVFISVKDKDKPKIYSVAKQLADMGFKIVSTEGTYRFLREKGIPVELVYKLQEGRrPNIGD 1002
54222889************************************************999876999** PP
TIGR01369 1001 llkeeeielvinltskkkkaaekgykirreaveykvplvteletaeallea 1051
l+k++e+ l+in+++ ++++++++y+irr av+y++p+ t++++ae++++a
lcl|NCBI__GCF_000185805.1:WP_013538311.1 1003 LIKNGEVCLIINTPT-GTRSKRDAYSIRRLAVNYGIPYYTTVRGAEMAVRA 1052
************998.778999************************99987 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1052 nodes)
Target sequences: 1 (1073 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: 0.08u 0.03s 00:00:00.11 Elapsed: 00:00:00.11
# Mc/sec: 9.84
//
[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