Alignments for a candidate for carB in Sulfurihydrogenibium subterraneum DSM 15120

GapMind for Amino acid biosynthesis

Alignments for a candidate for carB in Sulfurihydrogenibium subterraneum DSM 15120

Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate WP_028949747.1 Q385_RS0100240 carbamoyl-phosphate synthase large subunit

Query= BRENDA::P00968
         (1073 letters)



>NCBI__GCF_000619805.1:WP_028949747.1
          Length = 559

 Score =  654 bits (1688), Expect = 0.0
 Identities = 340/548 (62%), Positives = 421/548 (76%), Gaps = 8/548 (1%)

Query: 1   MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
           MPKRTDI++IL++G+GPIVIGQA EFDYSG Q  KAL+EEGYRVILVNSNPATIMTDP +
Sbjct: 1   MPKRTDIETILLIGSGPIVIGQAAEFDYSGTQGAKALKEEGYRVILVNSNPATIMTDPNI 60

Query: 61  ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
           AD TYIEP+   V+ KIIEKERPDA+LPT+GGQTALN A++L  +G+L+++ V +IGA  
Sbjct: 61  ADRTYIEPLITPVLEKIIEKERPDAILPTLGGQTALNLAIDLYEKGILDKYNVELIGAKY 120

Query: 121 DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180
           + I KAEDR  F  AM+ IGL   +S +  ++ EA  V   +GFP IIRPSFT+GG+GG 
Sbjct: 121 EVIKKAEDRDLFKKAMENIGLSMPKSAVVKSVAEAEEVIDWIGFPVIIRPSFTLGGTGGS 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 RFDFAKFPEADPTLTTMMKSVGEVMAIGRTFKESLQKALRSLELGRYGF--YMGLENIDE 417

Query: 421 LTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEVG 480
            T ++ ++     DR+WYIA+AFR G +V+ +  L++ID+WFL QI+E++  E  ++   
Sbjct: 418 NT-LKEKIIKPNPDRLWYIAEAFRKGYTVEEINKLSHIDKWFLNQIKEIIDYELYLSTKT 476

Query: 481 ITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATDT 540
           I  +    L + K+ GF+D  LA+L    E E+RK +    +   YK VDTCAAEF   T
Sbjct: 477 IDTITDQELEKAKQWGFSDRELARLLKTTEEEVRKRK----IIVSYKVVDTCAAEFEAFT 532

Query: 541 AYMYSTYE 548
            Y YS+YE
Sbjct: 533 PYYYSSYE 540



 Score =  233 bits (595), Expect = 2e-65
 Identities = 147/393 (37%), Positives = 214/393 (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   TDIETILLIGSGPIVIGQAAEFDYSGTQGAKALKEEGYRVILVNSNPATIMTDPNIADRT 64

Query: 617 YFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAAG------VPVIGTSPDAID 670
           Y EP+    + +I+  E+P  ++   GGQT L LA  L   G      V +IG   + I 
Sbjct: 65  YIEPLITPVLEKIIEKERPDAILPTLGGQTALNLAIDLYEKGILDKYNVELIGAKYEVIK 124

Query: 671 RAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYPLVVRPSYVLGGRAMEIVYD 730
           +AEDR+ F+ A+E + L  P +A V ++  A E    IG+P+++RPS+ LGG    I Y+
Sbjct: 125 KAEDRDLFKKAMENIGLSMPKSAVVKSVAEAEEVIDWIGFPVIIRPSFTLGGTGGSIAYN 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  DP L   M+S GEVM +GRTF E+  KA
Sbjct: 365 KFPEADPTLTTMMKSVGEVMAIGRTFKESLQKA 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: 1594
Number of extensions: 65
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_037919276.1 Q385_RS08730 carbamoyl-phosphate synthase large subunit

Query= BRENDA::P00968
         (1073 letters)



>NCBI__GCF_000619805.1:WP_037919276.1
          Length = 528

 Score =  578 bits (1490), Expect = e-169
 Identities = 291/530 (54%), Positives = 381/530 (71%), Gaps = 27/530 (5%)

Query: 560  EKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMVNCNPETVSTDYDTSDRLYFE 619
            +K+++LG GPNRIGQG+EFDY CVH   +LRE+GY+ IMVNCNPETVSTDYDTSD+L+FE
Sbjct: 2    KKVIILGSGPNRIGQGVEFDYACVHCVWSLREEGYQAIMVNCNPETVSTDYDTSDKLFFE 61

Query: 620  PVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAAGVPVIGTSPDAIDRAEDRERFQ 679
            P+ LEDVL I+  EKP GV+VQ+GGQTPLKLA+ LE   VP++GTSP++ID AEDRERF+
Sbjct: 62   PIVLEDVLNIIEREKPDGVVVQFGGQTPLKLAKPLEKLNVPILGTSPESIDIAEDRERFR 121

Query: 680  HAVERLKLKQPANATVTAIEMAVEKAKEIGYPLVVRPSYVLGGRAMEIVYDEADLRRYFQ 739
              +  L LKQP +    + E A++ A+ IGYP++VRPSYVLGGRAM +VYD ++L  Y Q
Sbjct: 122  DLIISLGLKQPKSGVARSKEEAIQIAENIGYPVLVRPSYVLGGRAMRLVYDTSELIEYIQ 181

Query: 740  TAVSVSNDAPVLLDHFLDDAVEVDVDAICDGEMVLIGGIMEHIEQAGVHSGDSACSLPAY 799
             AVSV+ D P+L+D FLD ++EVDVD +CDG+ VL+G +MEHIE+AG+HSGDSA  +P Y
Sbjct: 182  EAVSVTEDKPILIDKFLDGSIEVDVDCVCDGDDVLVGAVMEHIEEAGIHSGDSATCIPHY 241

Query: 800  TLSQEIQDVMRQQVQKLAFELQVRGLMNVQFAVKNNEVYLIEVNPRAARTVPFVSKATGV 859
            TL  E+   ++QQ +KLA  L   GL+N+Q+A+K+ E+Y+IE NPRA+RTVPFVSKA G 
Sbjct: 242  TLDDEVVIKIKQQSKKLAKALNTIGLINIQYAIKDGEIYVIEANPRASRTVPFVSKAIGY 301

Query: 860  PLAKVAARVMAGKSLAEQGVTKEVIP-------------------PYYSVKEVVLPFNKF 900
            PLAK+A++VM GK L      +E++P                   PYY+VKEVV P+N+F
Sbjct: 302  PLAKIASKVMVGKKL------REIVPQVFQIKDFHPASDFLPVDFPYYAVKEVVFPWNRF 355

Query: 901  PGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALLSVREGDKERVVDL 960
            P VDP+LGPEM+STGEVMG+ + F  A+ KAQ GS   + + G   +SV + DK +V+D+
Sbjct: 356  PEVDPVLGPEMKSTGEVMGIDKDFGLAYWKAQAGSGQILPQSGNIFISVADKDKPQVIDI 415

Query: 961  AAKLLKQGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIKNGEYTYIINTTSGR 1020
            A +LL  GF++ AT GT   L E GI   LVNK+ E RP+I DRIKNGE   IINT SG+
Sbjct: 416  AKQLLDLGFKIYATSGTYRFLQENGIQATLVNKLSEERPNIVDRIKNGEIAMIINTPSGK 475

Query: 1021 RAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNA--DATEKVISVQEM 1068
            R   D+  IRRSA+  K  Y TT+ G  A  MA+ +  D    VI++Q+M
Sbjct: 476  RERSDAYYIRRSAVATKTPYFTTIRGASAAVMAIKSYKDKGLNVIALQDM 525



 Score =  246 bits (629), Expect = 2e-69
 Identities = 153/437 (35%), Positives = 240/437 (54%), Gaps = 25/437 (5%)

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  EPIVLEDVLNIIEREKPDGVVVQFGGQTPLKLAKPLEK------LNVPILGTSPESIDIA 114

Query: 127 EDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGGIAYNRE 186
           EDR RF   +  +GL+  +SG+A + EEA+ +A ++G+P ++RPS+ +GG    + Y+  
Sbjct: 115 EDRERFRDLIISLGLKQPKSGVARSKEEAIQIAENIGYPVLVRPSYVLGGRAMRLVYDTS 174

Query: 187 EFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAMGIHTGD 246
           E  E     + ++  K +LID+ L G  E +++ V D  D+ ++   +E+ +  GIH+GD
Sbjct: 175 ELIEYIQEAVSVTEDKPILIDKFLDGSIEVDVDCVCD-GDDVLVGAVMEHIEEAGIHSGD 233

Query: 247 SITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEMNPRVSR 306
           S T  P  TL D+    ++  S  + + +    G  N+Q+A+  K+G + VIE NPR SR
Sbjct: 234 SATCIPHYTLDDEVVIKIKQQSKKLAKALNT-IGLINIQYAI--KDGEIYVIEANPRASR 290

Query: 307 SSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIPR----- 361
           +    SKA G+P+AK+A+K+ VG  L E++  +   +    F P+ D++    P      
Sbjct: 291 TVPFVSKAIGYPLAKIASKVMVGKKLREIVPQVFQIK---DFHPASDFLPVDFPYYAVKE 347

Query: 362 --FNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRG----LEVGATGFDPKVSL 415
             F + +F   +  L  +MKS GEVM I +    +  KA  G    L      F      
Sbjct: 348 VVFPWNRFPEVDPVLGPEMKSTGEVMGIDKDFGLAYWKAQAGSGQILPQSGNIFISVADK 407

Query: 416 DDPEALTKIRRELKDAG 432
           D P+ +  I ++L D G
Sbjct: 408 DKPQVI-DIAKQLLDLG 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: 1403
Number of extensions: 58
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 Jul 25 2024. The underlying query database was built on Jul 25 2024.

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About GapMind

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis