Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate WP_012674766.1 SULAZ_RS08345 carbamoyl-phosphate synthase large subunit
Query= BRENDA::P00968 (1073 letters) >NCBI__GCF_000021545.1:WP_012674766.1 Length = 559 Score = 656 bits (1693), Expect = 0.0 Identities = 342/548 (62%), Positives = 420/548 (76%), Gaps = 8/548 (1%) Query: 1 MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60 MPKRTDI++IL++G+GPI+IGQA EFDYSG Q KAL+EEGYRVILVNSNPATIMTDP + Sbjct: 1 MPKRTDIETILLIGSGPIIIGQAAEFDYSGTQGAKALKEEGYRVILVNSNPATIMTDPNI 60 Query: 61 ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120 AD TYIEP+ V+ KIIEKERPDA+LPT+GGQTALN A+EL +G+L+++ V +IGA Sbjct: 61 ADRTYIEPLITPVLEKIIEKERPDAILPTLGGQTALNLAIELYEKGILDKYNVELIGAKY 120 Query: 121 DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180 + I KAEDR F AM+ IGL +S + ++ EA V +GFP IIRPSFT+GG+GG Sbjct: 121 EVIKKAEDRDLFKKAMENIGLSMPKSAVVKSIAEAEEVIDWIGFPVIIRPSFTLGGTGGS 180 Query: 181 IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM 240 IAYNREEF GLD SP E+L++ES+IGWKE+EMEV+RDKNDNC+I+CSIEN D M Sbjct: 181 IAYNREEFYPKVKAGLDASPIHEVLLEESVIGWKEFEMEVMRDKNDNCVIICSIENLDPM 240 Query: 241 GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM 300 G+HTGDSIT+APA TL+D+EYQI+RN S+AV+REIGVETGGSNVQF+ NPK G VIEM Sbjct: 241 GVHTGDSITIAPAMTLSDREYQILRNYSIAVMREIGVETGGSNVQFSQNPKTGEFYVIEM 300 Query: 301 NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP 360 NPRVSRSSALASKATGFPIAK+AAKLAVGYTLDEL NDIT +TPASFEP+IDYVV KIP Sbjct: 301 NPRVSRSSALASKATGFPIAKIAAKLAVGYTLDELPNDIT-KKTPASFEPTIDYVVVKIP 359 Query: 361 RFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKVSLDDPEA 420 RF+F KF A+ LTT MKSVGEVMAIGRT +ESLQKALR LE+G GF + L++ + Sbjct: 360 RFDFAKFPEADKTLTTMMKSVGEVMAIGRTFKESLQKALRSLELGRYGF--YMGLENIDE 417 Query: 421 LTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEVG 480 T ++ + DR+WYIA+AFR G +V+ V L++ID+WFL QI+E++ E ++ Sbjct: 418 NT-LKENIIKPNPDRLWYIAEAFRRGYTVEEVNQLSHIDKWFLNQIKEIIDYEIYLSTKT 476 Query: 481 ITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATDT 540 I + L + K+ GF+D LA+L E E+RK R + YK VDTCAAEF T Sbjct: 477 IETITDQELEKAKQWGFSDRELARLLKTTEEEVRKRR----VAVSYKVVDTCAAEFEAFT 532 Query: 541 AYMYSTYE 548 Y YS+YE Sbjct: 533 PYYYSSYE 540 Score = 231 bits (589), Expect = 1e-64 Identities = 147/393 (37%), Positives = 213/393 (54%), Gaps = 18/393 (4%) Query: 557 TDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMVNCNPETVSTDYDTSDRL 616 TD E I+++G GP IGQ EFDY + AL+E+GY I+VN NP T+ TD + +DR Sbjct: 5 TDIETILLIGSGPIIIGQAAEFDYSGTQGAKALKEEGYRVILVNSNPATIMTDPNIADRT 64 Query: 617 YFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAAG------VPVIGTSPDAID 670 Y EP+ + +I+ E+P ++ GGQT L LA L G V +IG + I Sbjct: 65 YIEPLITPVLEKIIEKERPDAILPTLGGQTALNLAIELYEKGILDKYNVELIGAKYEVIK 124 Query: 671 RAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYPLVVRPSYVLGGRAMEIVYD 730 +AEDR+ F+ A+E + L P +A V +I A E IG+P+++RPS+ LGG I Y+ Sbjct: 125 KAEDRDLFKKAMENIGLSMPKSAVVKSIAEAEEVIDWIGFPVIIRPSFTLGGTGGSIAYN 184 Query: 731 EADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICD-GEMVLIGGIMEHIEQAGVHS 789 + + + S VLL+ + E +++ + D + +I +E+++ GVH+ Sbjct: 185 REEFYPKVKAGLDASPIHEVLLEESVIGWKEFEMEVMRDKNDNCVIICSIENLDPMGVHT 244 Query: 790 GDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVR-GLMNVQFA--VKNNEVYLIEVNPRA 846 GDS PA TLS ++R + E+ V G NVQF+ K E Y+IE+NPR Sbjct: 245 GDSITIAPAMTLSDREYQILRNYSIAVMREIGVETGGSNVQFSQNPKTGEFYVIEMNPRV 304 Query: 847 ARTVPFVSKATGVPLAKVAARVMAGKSLAE--QGVTK------EVIPPYYSVKEVVLPFN 898 +R+ SKATG P+AK+AA++ G +L E +TK E Y VK F Sbjct: 305 SRSSALASKATGFPIAKIAAKLAVGYTLDELPNDITKKTPASFEPTIDYVVVKIPRFDFA 364 Query: 899 KFPGVDPLLGPEMRSTGEVMGVGRTFAEAFAKA 931 KFP D L M+S GEVM +GRTF E+ KA Sbjct: 365 KFPEADKTLTTMMKSVGEVMAIGRTFKESLQKA 397 Lambda K H 0.318 0.135 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: 1569 Number of extensions: 70 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 1073 Length of database: 559 Length adjustment: 41 Effective length of query: 1032 Effective length of database: 518 Effective search space: 534576 Effective search space used: 534576 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: 55 (25.8 bits)
Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate WP_012674887.1 SULAZ_RS00665 carbamoyl-phosphate synthase large subunit
Query= BRENDA::P00968 (1073 letters) >NCBI__GCF_000021545.1:WP_012674887.1 Length = 528 Score = 574 bits (1479), Expect = e-168 Identities = 287/533 (53%), Positives = 384/533 (72%), Gaps = 27/533 (5%) Query: 560 EKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMVNCNPETVSTDYDTSDRLYFE 619 +K+++LG GPNRIGQG+EFDY CVH +LRE+GY+ IMVNCNPETVSTDYDTSD+L+FE Sbjct: 2 KKVIILGSGPNRIGQGVEFDYACVHCVWSLREEGYQAIMVNCNPETVSTDYDTSDKLFFE 61 Query: 620 PVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAAGVPVIGTSPDAIDRAEDRERFQ 679 P+ LEDV I+ EKP GV+VQ+GGQTPLKLA+ LE VP++GTSP++ID AEDRERF+ Sbjct: 62 PIVLEDVFNIIEREKPDGVVVQFGGQTPLKLAKPLEKLNVPILGTSPESIDIAEDRERFR 121 Query: 680 HAVERLKLKQPANATVTAIEMAVEKAKEIGYPLVVRPSYVLGGRAMEIVYDEADLRRYFQ 739 + L LKQP + + E A++ A+EIGYP++VRPSYVLGGRAM +VYD ++L +Y + Sbjct: 122 DLIISLGLKQPESGIARSKEEALKIAEEIGYPVLVRPSYVLGGRAMRLVYDTSELLQYIE 181 Query: 740 TAVSVSNDAPVLLDHFLDDAVEVDVDAICDGEMVLIGGIMEHIEQAGVHSGDSACSLPAY 799 AV+V+ D P+L+D FLD ++EVDVD +CDG+ VL+G +MEHIE+AG+HSGDSA +P Y Sbjct: 182 EAVTVTEDKPILIDKFLDGSIEVDVDCVCDGDDVLVGAVMEHIEEAGIHSGDSATCIPHY 241 Query: 800 TLSQEIQDVMRQQVQKLAFELQVRGLMNVQFAVKNNEVYLIEVNPRAARTVPFVSKATGV 859 TL EI ++QQ +KLA L GL+N+Q+A+K+ E+Y+IE NPRA+RTVPFVSKA G Sbjct: 242 TLDDEIVVKIKQQSKKLAKALNTIGLINIQYAIKDGEIYVIEANPRASRTVPFVSKAIGY 301 Query: 860 PLAKVAARVMAGKSLAEQGVTKEVIP-------------------PYYSVKEVVLPFNKF 900 PLAK+A++VM GK L KE++P PYY+VKEVV P+N+F Sbjct: 302 PLAKIASKVMVGKKL------KEIVPQVFQIKDVHPASDFLSVDFPYYAVKEVVFPWNRF 355 Query: 901 PGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALLSVREGDKERVVDL 960 P VDP+LGPEM+STGEVMG+ + F A+ KAQ G+ + + G +SV + DK +++D+ Sbjct: 356 PEVDPILGPEMKSTGEVMGIDKDFGLAYWKAQAGAGQILPQSGNVFISVADKDKPQIIDI 415 Query: 961 AAKLLKQGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIKNGEYTYIINTTSGR 1020 A +LL GF++ AT GT L + GIN LVNK+ E RP+I DRIKN E IINT SG+ Sbjct: 416 AKQLLDLGFKIYATSGTYRFLQQNGINATLVNKLSEERPNIVDRIKNSEIAMIINTPSGK 475 Query: 1021 RAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNA--DATEKVISVQEMHAQ 1071 R D+ IRR+A+ K Y TT+ G A MA+ + + VI++Q+M A+ Sbjct: 476 RERSDAYYIRRAAVATKTPYFTTVRGASAAVMAIKSYKEKGLNVIALQDMEAK 528 Score = 247 bits (630), Expect = 2e-69 Identities = 157/434 (36%), Positives = 240/434 (55%), Gaps = 19/434 (4%) Query: 7 IKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEMADATYI 66 +K ++ILG+GP IGQ EFDY+ +LREEGY+ I+VN NP T+ TD + +D + Sbjct: 1 MKKVIILGSGPNRIGQGVEFDYACVHCVWSLREEGYQAIMVNCNPETVSTDYDTSDKLFF 60 Query: 67 EPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATADAIDKA 126 EPI E V IIE+E+PD V+ GGQT L A LE+ V ++G + ++ID A Sbjct: 61 EPIVLEDVFNIIEREKPDGVVVQFGGQTPLKLAKPLEK------LNVPILGTSPESIDIA 114 Query: 127 EDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGGIAYNRE 186 EDR RF + +GL+ SGIA + EEAL +A ++G+P ++RPS+ +GG + Y+ Sbjct: 115 EDRERFRDLIISLGLKQPESGIARSKEEALKIAEEIGYPVLVRPSYVLGGRAMRLVYDTS 174 Query: 187 EFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAMGIHTGD 246 E + + ++ K +LID+ L G E +++ V D D+ ++ +E+ + GIH+GD Sbjct: 175 ELLQYIEEAVTVTEDKPILIDKFLDGSIEVDVDCVCD-GDDVLVGAVMEHIEEAGIHSGD 233 Query: 247 SITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEMNPRVSR 306 S T P TL D+ ++ S + + + G N+Q+A+ K+G + VIE NPR SR Sbjct: 234 SATCIPHYTLDDEIVVKIKQQSKKLAKALNT-IGLINIQYAI--KDGEIYVIEANPRASR 290 Query: 307 SSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRT--PASFEPSID--YVVTKIPRF 362 + SKA G+P+AK+A+K+ VG L E++ + + PAS S+D Y K F Sbjct: 291 TVPFVSKAIGYPLAKIASKVMVGKKLKEIVPQVFQIKDVHPASDFLSVDFPYYAVKEVVF 350 Query: 363 NFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRG----LEVGATGFDPKVSLDDP 418 + +F + L +MKS GEVM I + + KA G L F D P Sbjct: 351 PWNRFPEVDPILGPEMKSTGEVMGIDKDFGLAYWKAQAGAGQILPQSGNVFISVADKDKP 410 Query: 419 EALTKIRRELKDAG 432 + + I ++L D G Sbjct: 411 Q-IIDIAKQLLDLG 423 Lambda K H 0.318 0.135 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: 1437 Number of extensions: 57 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 1073 Length of database: 528 Length adjustment: 40 Effective length of query: 1033 Effective length of database: 488 Effective search space: 504104 Effective search space used: 504104 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: 55 (25.8 bits)
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