Align Carbamoyl-phosphate synthase pyrimidine-specific large chain; Carbamoyl-phosphate synthetase ammonia chain; EC 6.3.5.5 (characterized)
to candidate WP_078430672.1 BK574_RS26025 carbamoyl-phosphate synthase large subunit
Query= SwissProt::P25994
(1071 letters)
>NCBI__GCF_002019605.1:WP_078430672.1
Length = 1062
Score = 1633 bits (4229), Expect = 0.0
Identities = 815/1061 (76%), Positives = 933/1061 (87%)
Query: 1 MPKRVDINKILVIGSGPIIIGQAAEFDYAGTQACLALKEEGYEVILVNSNPATIMTDTEM 60
MPKR DINKILVIGSGPI+IGQAAEFDYAGTQAC ALKEEGYEVIL+NSNPATIMTDT M
Sbjct: 1 MPKRTDINKILVIGSGPIVIGQAAEFDYAGTQACQALKEEGYEVILINSNPATIMTDTTM 60
Query: 61 ADRVYIEPLTPEFLTRIIRKERPDAILPTLGGQTGLNLAVELSERGVLAECGVEVLGTKL 120
ADRVYIEP+T EF++RIIR+ERPD +L TLGGQTGLN+AVEL E G+L E +E+LGT L
Sbjct: 61 ADRVYIEPITYEFVSRIIRQERPDGLLATLGGQTGLNMAVELEESGILKEYNIELLGTHL 120
Query: 121 SAIQQAEDRDLFRTLMNELNEPVPESEIIHSLEEAEKFVSQIGFPVIVRPAYTLGGTGGG 180
AI+QAEDRDLFR+LMNELNEPVP+S+I+H+LEEA +FV +IG+P+IVRPAYTLGGTGGG
Sbjct: 121 DAIKQAEDRDLFRSLMNELNEPVPDSDIVHNLEEAYRFVERIGYPIIVRPAYTLGGTGGG 180
Query: 181 ICSNETELKEIVENGLKLSPVHQCLLEKSIAGYKEIEYEVMRDSQDHAIVVCNMENIDPV 240
+ NE +L EIV +GLK SPV QCLLEKSIAG+KE+EYEVMRD ++ AIVVCNMENIDPV
Sbjct: 181 LVYNEEDLIEIVTSGLKYSPVTQCLLEKSIAGFKEVEYEVMRDGKNQAIVVCNMENIDPV 240
Query: 241 GIHTGDSIVVAPSQTLSDREYQLLRNVSLKLIRALGIEGGCNVQLALDPDSFQYYIIEVN 300
G+HTGDSIVVAPSQTLSDREYQ+LRN SLK+IRALGIEGGCNVQ ALDPDS+QYYIIEVN
Sbjct: 241 GVHTGDSIVVAPSQTLSDREYQMLRNSSLKIIRALGIEGGCNVQFALDPDSYQYYIIEVN 300
Query: 301 PRVSRSSALASKATGYPIAKLAAKIAVGLSLDEMMNPVTGKTYAAFEPALDYVVSKIPRW 360
PRVSRSSALASKATGYPIAK+AAKIAVG +LDE+MNP+T TYA+FEPALDYVVSKIPRW
Sbjct: 301 PRVSRSSALASKATGYPIAKIAAKIAVGYALDEIMNPITKTTYASFEPALDYVVSKIPRW 360
Query: 361 PFDKFESANRKLGTQMKATGEVMAIGRTLEESLLKAVRSLEADVYHLELKDAADISDELL 420
PFDKFESANR LGTQMKATGEVMAIGR LEESLLKA+RSLEA+V+HLE + ++ +
Sbjct: 361 PFDKFESANRTLGTQMKATGEVMAIGRNLEESLLKAIRSLEANVFHLERSGLETLENDEI 420
Query: 421 EKRIKKAGDERLFYLAEAYRRGYTVEDLHEFSAIDVFFLHKLFGIVQFEKELKANAGDTD 480
EKR+ A DERLF + EA+RRGYTVE L + S ID FFLHK+ IV+ EK LK + G+ +
Sbjct: 421 EKRVAVADDERLFVIGEAFRRGYTVEQLWKLSQIDRFFLHKMEDIVKLEKLLKESKGNIE 480
Query: 481 VLRRAKELGFSDQYISREWKMKESELYSLRKQAGIAPVFKMVDTCAAEFESETPYFYSTY 540
+L AKE GF+D I++ W+M+E +++ LR++ G+ PV+KMVDTCAAEFES TPYFY TY
Sbjct: 481 LLTEAKEKGFADVTIAKLWEMEEGDIFDLREKEGLMPVYKMVDTCAAEFESATPYFYGTY 540
Query: 541 EEENESVVTDKKSVMVLGSGPIRIGQGVEFDYATVHSVWAIKQAGYEAIIVNNNPETVST 600
E+ENES ++DKKS++VLGSGPIRIGQG+EFDYATVH+VWAIK+AGYEAII+NNNPETVST
Sbjct: 541 EDENESFISDKKSILVLGSGPIRIGQGIEFDYATVHTVWAIKEAGYEAIIINNNPETVST 600
Query: 601 DFSISDKLYFEPLTIEDVMHIIDLEQPMGVVVQFGGQTAINLADELSARGVKILGTSLED 660
DFS SDKLYFEPLT+EDV+H+I EQP GV+VQFGGQTAINLA L+ARGVKILGT+LED
Sbjct: 601 DFSTSDKLYFEPLTLEDVLHVIKQEQPEGVIVQFGGQTAINLAAGLAARGVKILGTALED 660
Query: 661 LDRAEDRDKFEQALGELGVPQPLGKTATSVNQAVSIASDIGYPVLVRPSYVLGGRAMEIV 720
+DRAEDRDKFEQ L EL + QPLGKTATSV QAV IAS IGYPVLVRPSYVLGGRAMEIV
Sbjct: 661 MDRAEDRDKFEQTLQELAILQPLGKTATSVEQAVKIASGIGYPVLVRPSYVLGGRAMEIV 720
Query: 721 YHEEELLHYMKNAVKINPQHPVLIDRYLTGKEIEVDAVSDGETVVIPGIMEHIERAGVHS 780
Y E ELL+YM+NAVKINP+HPVL+DRYLTGKEIEVDA+SDGE V IPGIMEHIERAGVHS
Sbjct: 721 YKEAELLNYMENAVKINPKHPVLVDRYLTGKEIEVDAISDGENVYIPGIMEHIERAGVHS 780
Query: 781 GDSIAVYPPQSLTEDIKKKIEQYTIALAKGLNIVGLLNIQFVLSQGEVYVLEVNPRSSRT 840
GDSIAVYPPQ+L+ +IK+K+ + TIALA+GL IVGLLNIQFVL EVYVLEVNPRSSRT
Sbjct: 781 GDSIAVYPPQTLSTEIKEKVIERTIALARGLKIVGLLNIQFVLHDNEVYVLEVNPRSSRT 840
Query: 841 VPFLSKITGIPMANLATKIILGQKLAAFGYTEGLQPEQQGVFVKAPVFSFAKLRRVDITL 900
VPFLSKITG+ MANLATK ILG+KL GY G PE + V VK PVFSFAKLRRVDI+L
Sbjct: 841 VPFLSKITGVAMANLATKAILGKKLPELGYETGYHPEGKEVSVKVPVFSFAKLRRVDISL 900
Query: 901 GPEMKSTGEVMGKDSTLEKALYKALIASGIQIPNYGSVLLTVADKDKEEGLAIAKRFHAI 960
GPEMKSTGEVMG+D TLEKALYK LIASG++IP +GSVL T+ADKDKEEGL + RFH I
Sbjct: 901 GPEMKSTGEVMGRDYTLEKALYKGLIASGMKIPKFGSVLFTIADKDKEEGLELVHRFHRI 960
Query: 961 GYNILATEGTAGYLKEASIPAKVVGKIGQDGPNLLDVIRNGEAQFVINTLTKGKQPARDG 1020
GYNILATEGTA +KE +IP V KIG + PNLLDVIR G+AQFVINT +KGKQPARDG
Sbjct: 961 GYNILATEGTAQMIKELNIPVTTVNKIGSEKPNLLDVIREGQAQFVINTFSKGKQPARDG 1020
Query: 1021 FRIRRESVENGVACLTSLDTAEAILRVLESMTFRADQMPAV 1061
FRIRRE+VENGV CLTSLDTAEA+L+V+ES+TF ++ MPA+
Sbjct: 1021 FRIRREAVENGVVCLTSLDTAEALLKVIESITFASESMPAM 1061
Lambda K H
0.316 0.135 0.377
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: 3177
Number of extensions: 129
Number of successful extensions: 11
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: 1071
Length of database: 1062
Length adjustment: 45
Effective length of query: 1026
Effective length of database: 1017
Effective search space: 1043442
Effective search space used: 1043442
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: 58 (26.9 bits)
Align candidate WP_078430672.1 BK574_RS26025 (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.1293250.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 1612.1 1.3 0 1611.9 1.3 1.0 1 NCBI__GCF_002019605.1:WP_078430672.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002019605.1:WP_078430672.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1611.9 1.3 0 0 1 1051 [. 2 1047 .. 2 1048 .. 0.99
Alignments for each domain:
== domain 1 score: 1611.9 bits; conditional E-value: 0
TIGR01369 1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePltve 71
pkr+di+k+lviGsGpivigqAaEFDY+G+qa++alkeeg+ev+L+nsn+At+mtd+++ad+vYieP+t e
NCBI__GCF_002019605.1:WP_078430672.1 2 PKRTDINKILVIGSGPIVIGQAAEFDYAGTQACQALKEEGYEVILINSNPATIMTDTTMADRVYIEPITYE 72
689******************************************************************** PP
TIGR01369 72 avekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealkeineev 142
+v++ii++ErpD++l+tlGGqt+Ln+avelee+G+L++y+++llGt+++aik+aedR++F+++++e+ne+v
NCBI__GCF_002019605.1:WP_078430672.1 73 FVSRIIRQERPDGLLATLGGQTGLNMAVELEESGILKEYNIELLGTHLDAIKQAEDRDLFRSLMNELNEPV 143
*********************************************************************** PP
TIGR01369 143 akseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikqvlvekslagwk 213
++s+iv++ eea +++e+igyP+ivR+a+tlgGtG+g+++nee+l e+v ++lk sp++q+l+eks+ag+k
NCBI__GCF_002019605.1:WP_078430672.1 144 PDSDIVHNLEEAYRFVERIGYPIIVRPAYTLGGTGGGLVYNEEDLIEIVTSGLKYSPVTQCLLEKSIAGFK 214
*********************************************************************** PP
TIGR01369 214 EiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslkiirelgvegecnvqf 284
E+EyEv+RD k+++i+vcn+En+Dp+GvHtGdsivvaPsqtL+d+eyq+lR++slkiir+lg+eg+cnvqf
NCBI__GCF_002019605.1:WP_078430672.1 215 EVEYEVMRDGKNQAIVVCNMENIDPVGVHTGDSIVVAPSQTLSDREYQMLRNSSLKIIRALGIEGGCNVQF 285
*********************************************************************** PP
TIGR01369 285 aldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelkndvtketvAsfEPslDYvvvk 355
aldP+s++y++iEvnpRvsRssALAskAtGyPiAk+aak+avGy Lde++n++tk+t+AsfEP+lDYvv+k
NCBI__GCF_002019605.1:WP_078430672.1 286 ALDPDSYQYYIIEVNPRVSRSSALASKATGYPIAKIAAKIAVGYALDEIMNPITKTTYASFEPALDYVVSK 356
*********************************************************************** PP
TIGR01369 356 iPrwdldkfekvdrklgtqmksvGEvmaigrtfeealqkalrsleekllglklkekeaesdeeleealkkp 426
iPrw++dkfe+++r+lgtqmk++GEvmaigr++ee+l+ka+rsle+++ +l+ + e+ +++e+e+++ +
NCBI__GCF_002019605.1:WP_078430672.1 357 IPRWPFDKFESANRTLGTQMKATGEVMAIGRNLEESLLKAIRSLEANVFHLERSGLETLENDEIEKRVAVA 427
*********************************************************************** PP
TIGR01369 427 ndrRlfaiaealrrgvsveevyeltkidrffleklkklvelekeleeeklkelkkellkkakklGfsdeqi 497
+d+Rlf+i ea+rrg++ve++++l++idrffl+k++++v+lek l+e+k + ell++ak++Gf+d +i
NCBI__GCF_002019605.1:WP_078430672.1 428 DDERLFVIGEAFRRGYTVEQLWKLSQIDRFFLHKMEDIVKLEKLLKESKGN---IELLTEAKEKGFADVTI 495
*********************************************966555...9**************** PP
TIGR01369 498 aklvkvseaevrklrkelgivpvvkrvDtvaaEfeaktpYlYstyeeekddvevtekkkvlvlGsGpiRig 568
akl++++e ++ +lr++ g++pv+k+vDt+aaEfe++tpY+Y tye+e +++ +++kk++lvlGsGpiRig
NCBI__GCF_002019605.1:WP_078430672.1 496 AKLWEMEEGDIFDLREKEGLMPVYKMVDTCAAEFESATPYFYGTYEDE-NESFISDKKSILVLGSGPIRIG 565
************************************************.9999****************** PP
TIGR01369 569 qgvEFDycavhavlalreagyktilinynPEtvstDydiadrLyFeeltvedvldiiekekvegvivqlgG 639
qg+EFDy++vh+v+a++eagy++i+in+nPEtvstD++++d+LyFe+lt+edvl++i++e++egvivq+gG
NCBI__GCF_002019605.1:WP_078430672.1 566 QGIEFDYATVHTVWAIKEAGYEAIIINNNPETVSTDFSTSDKLYFEPLTLEDVLHVIKQEQPEGVIVQFGG 636
*********************************************************************** PP
TIGR01369 640 qtalnlakeleeagvkilGtsaesidraEdRekFsklldelgikqpkgkeatsveeakeiakeigyPvlvR 710
qta+nla l+++gvkilGt e++draEdR+kF++ l+el i qp gk+atsve+a++ia+ igyPvlvR
NCBI__GCF_002019605.1:WP_078430672.1 637 QTAINLAAGLAARGVKILGTALEDMDRAEDRDKFEQTLQELAILQPLGKTATSVEQAVKIASGIGYPVLVR 707
*********************************************************************** PP
TIGR01369 711 psyvlgGrameiveneeeleryleeavevskekPvlidkyledavEvdvDavadgeevliagileHiEeaG 781
psyvlgGrameiv++e+el +y+e+av++++++Pvl+d+yl+ ++E++vDa++dge+v+i+gi+eHiE+aG
NCBI__GCF_002019605.1:WP_078430672.1 708 PSYVLGGRAMEIVYKEAELLNYMENAVKINPKHPVLVDRYLT-GKEIEVDAISDGENVYIPGIMEHIERAG 777
******************************************.**************************** PP
TIGR01369 782 vHsGDstlvlppqklseevkkkikeivkkiakelkvkGllniqfvvkdeevyviEvnvRasRtvPfvskal 852
vHsGDs++v+ppq+ls+e+k+k+ e + ++a+ lk++Gllniqfv++d+evyv+Evn+R+sRtvPf+sk++
NCBI__GCF_002019605.1:WP_078430672.1 778 VHSGDSIAVYPPQTLSTEIKEKVIERTIALARGLKIVGLLNIQFVLHDNEVYVLEVNPRSSRTVPFLSKIT 848
*********************************************************************** PP
TIGR01369 853 gvplvklavkvllgkkleelekgvkkekksklvavkaavfsfsklagvdvvlgpemkstGEvmgigrdlee 923
gv +++la+k++lgkkl el++ ++++ k v+vk++vfsf+kl++vd+ lgpemkstGEvmg +++le+
NCBI__GCF_002019605.1:WP_078430672.1 849 GVAMANLATKAILGKKLPELGYETGYHPEGKEVSVKVPVFSFAKLRRVDISLGPEMKSTGEVMGRDYTLEK 919
*********************************************************************** PP
TIGR01369 924 allkallaskakikkkgsvllsvkdkdkeellelakklaekglkvyategtakvleeagikaevvlkvsee 994
al+k l+as++ki+k gsvl +++dkdkee lel+++++++g++++ategta++++e +i +++v+k+ +e
NCBI__GCF_002019605.1:WP_078430672.1 920 ALYKGLIASGMKIPKFGSVLFTIADKDKEEGLELVHRFHRIGYNILATEGTAQMIKELNIPVTTVNKIGSE 990
*********************************************************************** PP
TIGR01369 995 aekilellkeeeielvinltskkkkaaekgykirreaveykvplvteletaeallea 1051
++++l++++e+++++vin+ sk+k+ a++g++irreave++v ++t+l+taeall++
NCBI__GCF_002019605.1:WP_078430672.1 991 KPNLLDVIREGQAQFVINTFSKGKQPARDGFRIRREAVENGVVCLTSLDTAEALLKV 1047
****************************************************99986 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1052 nodes)
Target sequences: 1 (1062 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: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 28.15
//
[ok]
This GapMind analysis is from Jul 25 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