Alignments for a candidate for carB in Chlorobium limicola DSM 245

GapMind for Amino acid biosynthesis

Alignments for a candidate for carB in Chlorobium limicola DSM 245

Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate WP_012465441.1 CLIM_RS02385 carbamoyl-phosphate synthase large subunit

Query= BRENDA::P00968
         (1073 letters)



>NCBI__GCF_000020465.1:WP_012465441.1
          Length = 495

 Score =  595 bits (1535), Expect = e-174
 Identities = 309/489 (63%), Positives = 376/489 (76%), Gaps = 11/489 (2%)

Query: 1   MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
           MPKR DI+SIL++GAGPIVIGQACEFDYSG QAC+AL+E+GYRVILVNSNPATIMTD EM
Sbjct: 1   MPKREDIQSILVIGAGPIVIGQACEFDYSGTQACRALKEDGYRVILVNSNPATIMTDIEM 60

Query: 61  ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
           ADATYIEPI  E VRKIIEKE+PDA+LPTMGGQTALN A+ L   G+LE  GV +IGA  
Sbjct: 61  ADATYIEPITPEYVRKIIEKEKPDALLPTMGGQTALNTAVTLAESGILERNGVELIGAKL 120

Query: 121 DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180
            AI KAE+R  F  AMKKIGLE A+       +EA     ++G P +IRPSFT+GG+GGG
Sbjct: 121 RAIRKAENREFFSDAMKKIGLEMAKGFFVRNEKEAREALEEIGLPIVIRPSFTLGGTGGG 180

Query: 181 IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM 240
            A  + ++ E   RGL  SP  E+L++E L+GWKE+E+EV+RD  DN IIVCSIEN D M
Sbjct: 181 FAETKSDYYEAVRRGLAESPISEVLVEECLVGWKEFELEVIRDLADNVIIVCSIENVDPM 240

Query: 241 GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM 300
           G+HTGDSITVAPAQTLTD++YQ++R+AS+ ++REIGVETGGSN+QFA+NP+NGR++VIEM
Sbjct: 241 GVHTGDSITVAPAQTLTDRQYQVLRDASIRIIREIGVETGGSNIQFAINPENGRIVVIEM 300

Query: 301 NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP 360
           NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDE++NDIT   TPASFEP IDY V KIP
Sbjct: 301 NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDEILNDITKS-TPASFEPVIDYCVVKIP 359

Query: 361 RFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGF--DPKVSLDDP 418
           R++FEKF   + RL  QMKSVGEVMA GR  +E+LQK+LRGLE+G  G   D K  ++  
Sbjct: 360 RWDFEKFKNVDARLGVQMKSVGEVMAFGRNFREALQKSLRGLEIGRAGLGADGKDIMNVV 419

Query: 419 E--------ALTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELV 470
           +        A   I  ++K   ADR++Y+  AF+AG +VD V   T ID WFL  I ++V
Sbjct: 420 DMTQQQKMFAKEDILEKIKVPKADRMFYLRYAFQAGATVDEVHQSTKIDPWFLDNIRQIV 479

Query: 471 RLEEKVAEV 479
             E ++ E+
Sbjct: 480 EFEAELREL 488



 Score =  235 bits (600), Expect = 5e-66
 Identities = 159/421 (37%), Positives = 227/421 (53%), Gaps = 23/421 (5%)

Query: 558 DREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMVNCNPETVSTDYDTSDRLY 617
           D + I+V+G GP  IGQ  EFDY    A  AL+EDGY  I+VN NP T+ TD + +D  Y
Sbjct: 6   DIQSILVIGAGPIVIGQACEFDYSGTQACRALKEDGYRVILVNSNPATIMTDIEMADATY 65

Query: 618 FEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLA------RALEAAGVPVIGTSPDAIDR 671
            EP+T E V +I+  EKP  ++   GGQT L  A        LE  GV +IG    AI +
Sbjct: 66  IEPITPEYVRKIIEKEKPDALLPTMGGQTALNTAVTLAESGILERNGVELIGAKLRAIRK 125

Query: 672 AEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYPLVVRPSYVLGGRAMEIVYDE 731
           AE+RE F  A++++ L+      V   + A E  +EIG P+V+RPS+ LGG        +
Sbjct: 126 AENREFFSDAMKKIGLEMAKGFFVRNEKEAREALEEIGLPIVIRPSFTLGGTGGGFAETK 185

Query: 732 ADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICD-GEMVLIGGIMEHIEQAGVHSG 790
           +D     +  ++ S  + VL++  L    E +++ I D  + V+I   +E+++  GVH+G
Sbjct: 186 SDYYEAVRRGLAESPISEVLVEECLVGWKEFELEVIRDLADNVIIVCSIENVDPMGVHTG 245

Query: 791 DSACSLPAYTLSQEIQDVMRQQVQKLAFELQVR-GLMNVQFAV--KNNEVYLIEVNPRAA 847
           DS    PA TL+     V+R    ++  E+ V  G  N+QFA+  +N  + +IE+NPR +
Sbjct: 246 DSITVAPAQTLTDRQYQVLRDASIRIIREIGVETGGSNIQFAINPENGRIVVIEMNPRVS 305

Query: 848 RTVPFVSKATGVPLAKVAARVMAGKSLAE--QGVTK------EVIPPYYSVKEVVLPFNK 899
           R+    SKATG P+AKVAA++  G +L E    +TK      E +  Y  VK     F K
Sbjct: 306 RSSALASKATGFPIAKVAAKLAVGYTLDEILNDITKSTPASFEPVIDYCVVKIPRWDFEK 365

Query: 900 FPGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALLSVREGDKERVVD 959
           F  VD  LG +M+S GEVM  GR F EA  K+  G      + GRA L     D   VVD
Sbjct: 366 FKNVDARLGVQMKSVGEVMAFGRNFREALQKSLRG-----LEIGRAGLGADGKDIMNVVD 420

Query: 960 L 960
           +
Sbjct: 421 M 421


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: 1451
Number of extensions: 65
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: 495
Length adjustment: 40
Effective length of query: 1033
Effective length of database: 455
Effective search space:   470015
Effective search space used:   470015
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_012466868.1 CLIM_RS09890 carbamoyl-phosphate synthase large subunit

Query= BRENDA::P00968
         (1073 letters)



>NCBI__GCF_000020465.1:WP_012466868.1
          Length = 618

 Score =  538 bits (1385), Expect = e-157
 Identities = 291/592 (49%), Positives = 390/592 (65%), Gaps = 11/592 (1%)

Query: 489  LRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATDTAYMYSTYE 548
            L + K  GF+D +LA +    E  IR LR QY +  V+K VDTCAAEF   T Y YSTY+
Sbjct: 24   LIKAKEHGFSDCQLANIFKTTETVIRTLRKQYGVESVFKTVDTCAAEFDAKTPYHYSTYD 83

Query: 549  EECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMVNCNPETVST 608
            EE E+  S DR+K+++LGGGPNRIGQGIEFDYCCV A  ALRE GYETIMVNCNPETVST
Sbjct: 84   EENESVRS-DRKKVIILGGGPNRIGQGIEFDYCCVQAVFALREAGYETIMVNCNPETVST 142

Query: 609  DYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAAGVPVIGTSPDA 668
            DYD +D+LYFEP+T ED + I+  E+P GVIV +GGQTPLKL+  L+ AGV ++GTS   
Sbjct: 143  DYDIADKLYFEPLTFEDTIRIIEHEQPLGVIVSFGGQTPLKLSTKLDEAGVTILGTSSKG 202

Query: 669  IDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYPLVVRPSYVLGGRAMEIV 728
            ID AEDR++F   +E+L +  P   T    + A+   + IGYP++VRPSYVLGGRAM+I+
Sbjct: 203  IDLAEDRKKFGALLEKLDILHPDYGTAICFDEALAITERIGYPVLVRPSYVLGGRAMKII 262

Query: 729  YDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDGEMVLIGGIMEHIEQAGVH 788
            Y++  L+ Y   A+ +S   P+L+D FL+ AVE D+DAI D    +I GIM+H+E AG+H
Sbjct: 263  YNKDSLKEYVDQALFISEKYPLLIDRFLETAVEFDIDAIADTTDCVISGIMQHVEAAGIH 322

Query: 789  SGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLMNVQFAVKNNEVYLIEVNPRAAR 848
            SGDS   LP   +SQE+ + M+   + LA  L+V GLMNVQ+AV+N  VY+IEVNPRA+R
Sbjct: 323  SGDSTSILPYRNISQEVINTMKAYTRTLAEHLKVVGLMNVQYAVQNESVYVIEVNPRASR 382

Query: 849  TVPFVSKATGVPLAKVAARVMAGKSLAEQGV------TKEVIPPYYSVKEVVLPFNKFPG 902
            TVPFV KAT VP+ K+A RVM G+ L++           E+   + ++KE V PF+KF  
Sbjct: 383  TVPFVGKATAVPVVKIATRVMLGEKLSDLRKEYDLKDCDELGMKHMAIKEPVFPFSKFVK 442

Query: 903  VDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALLSVREGDK-ERVVDLA 961
                LGPEMRSTGE M +   F EAFAKA   +N  +   G   +SV + DK +R++ +A
Sbjct: 443  SGVYLGPEMRSTGEAMSLAEQFPEAFAKAYQAANMELPLSGSVFISVNDQDKSQRIIAIA 502

Query: 962  AKLLKQGFELDATHGTAIVLGEAGINPRLVNKV-HEGRPHIQDRIKNGEYTYIINTTSGR 1020
             +L +  F+L AT GT   L E GI  + V KV  EGRP+I D IK+G+  ++INT  G 
Sbjct: 503  KELYRMDFDLVATAGTHRFLIENGIECKKVFKVGEEGRPNIFDIIKHGKIDFVINTPRGE 562

Query: 1021 RAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNADATEK--VISVQEMHA 1070
            +A+ D   I  +++   V + TT+    A+  A++    ++  V S+QE  A
Sbjct: 563  KALHDEEAIGAASVLSNVPFVTTIEAAEASVQAIDCIRRQEFGVKSLQEYSA 614



 Score =  243 bits (619), Expect = 4e-68
 Identities = 147/429 (34%), Positives = 234/429 (54%), Gaps = 17/429 (3%)

Query: 4   RTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEMADA 63
           R+D K ++ILG GP  IGQ  EFDY   QA  ALRE GY  I+VN NP T+ TD ++AD 
Sbjct: 90  RSDRKKVIILGGGPNRIGQGIEFDYCCVQAVFALREAGYETIMVNCNPETVSTDYDIADK 149

Query: 64  TYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATADAI 123
            Y EP+ +E   +IIE E+P  V+ + GGQT L  + +      L+E GVT++G ++  I
Sbjct: 150 LYFEPLTFEDTIRIIEHEQPLGVIVSFGGQTPLKLSTK------LDEAGVTILGTSSKGI 203

Query: 124 DKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGGIAY 183
           D AEDR++F   ++K+ +     G A   +EALA+   +G+P ++RPS+ +GG    I Y
Sbjct: 204 DLAEDRKKFGALLEKLDILHPDYGTAICFDEALAITERIGYPVLVRPSYVLGGRAMKIIY 263

Query: 184 NREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAMGIH 243
           N++  +E   + L +S    LLID  L    E++++ + D  D C+I   +++ +A GIH
Sbjct: 264 NKDSLKEYVDQALFISEKYPLLIDRFLETAVEFDIDAIADTTD-CVISGIMQHVEAAGIH 322

Query: 244 TGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEMNPR 303
           +GDS ++ P + ++ +    M+  +  +   + V  G  NVQ+AV  +N  + VIE+NPR
Sbjct: 323 SGDSTSILPYRNISQEVINTMKAYTRTLAEHLKV-VGLMNVQYAV--QNESVYVIEVNPR 379

Query: 304 VSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIPRFN 363
            SR+     KAT  P+ K+A ++ +G  L +L  +          E  + ++  K P F 
Sbjct: 380 ASRTVPFVGKATAVPVVKIATRVMLGEKLSDLRKEYD---LKDCDELGMKHMAIKEPVFP 436

Query: 364 FEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRG----LEVGATGFDPKVSLDDPE 419
           F KF  +   L  +M+S GE M++     E+  KA +     L +  + F      D  +
Sbjct: 437 FSKFVKSGVYLGPEMRSTGEAMSLAEQFPEAFAKAYQAANMELPLSGSVFISVNDQDKSQ 496

Query: 420 ALTKIRREL 428
            +  I +EL
Sbjct: 497 RIIAIAKEL 505


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: 1492
Number of extensions: 75
Number of successful extensions: 10
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: 618
Length adjustment: 41
Effective length of query: 1032
Effective length of database: 577
Effective search space:   595464
Effective search space used:   595464
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: 56 (26.2 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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