Alignments for a candidate for carB in Sinorhizobium meliloti 1021

GapMind for Amino acid biosynthesis

Alignments for a candidate for carB in Sinorhizobium meliloti 1021

Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate SMc01215 SMc01215 carbamoyl phosphate synthase large subunit

Query= BRENDA::P00968
         (1073 letters)



>FitnessBrowser__Smeli:SMc01215
          Length = 1163

 Score = 1264 bits (3272), Expect = 0.0
 Identities = 683/1149 (59%), Positives = 814/1149 (70%), Gaps = 96/1149 (8%)

Query: 1    MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
            MPKR DIKSILI+GAGPIVIGQACEFDYSG QACKAL+EEGYRVILVNSNPATIMTDP +
Sbjct: 1    MPKRQDIKSILIIGAGPIVIGQACEFDYSGTQACKALKEEGYRVILVNSNPATIMTDPGL 60

Query: 61   ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
            ADATY+EPI  EVV KII KERPDA+LPTMGGQTALN AL L R GVL+ + V MIGA  
Sbjct: 61   ADATYVEPITPEVVAKIIAKERPDALLPTMGGQTALNTALSLRRMGVLDRYNVEMIGAKP 120

Query: 121  DAIDKAEDRRRFDVAMKKIGLETARSGIAHTME--------------------------- 153
            +AIDKAEDR  F  AM  IGLET +S +A+  +                           
Sbjct: 121  EAIDKAEDRALFREAMAHIGLETPKSRLANATDIKDHDRKSHEAERSALKAKLSGDELDK 180

Query: 154  ----------------------EALAVAA----DVGFPCIIRPSFTMGGSGGGIAYNREE 187
                                   A+A+AA    DVG P IIRPSFT+GG+GGGIAYNR E
Sbjct: 181  ALDELENQWNLGEGDRKQRYVNHAMAIAAQALDDVGLPAIIRPSFTLGGTGGGIAYNRSE 240

Query: 188  FEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAMGIHTGDS 247
            F EI   GLD SPT E+LI+ES++GWKEYEMEVVRDK DNCII+CSIEN D MG+HTGDS
Sbjct: 241  FFEIVGSGLDASPTTEVLIEESVLGWKEYEMEVVRDKADNCIIICSIENIDPMGVHTGDS 300

Query: 248  ITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEMNPRVSRS 307
            ITVAPA TLTDKEYQIMRNAS+AVLREIGVETGGSNVQFAVNP+NGRL+VIEMNPRVSRS
Sbjct: 301  ITVAPALTLTDKEYQIMRNASIAVLREIGVETGGSNVQFAVNPENGRLVVIEMNPRVSRS 360

Query: 308  SALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIPRFNFEKF 367
            SALASKATGFPIAK+AAKLAVGYTLDEL NDITGG TPASFEPSIDYVVTKIPRF FEKF
Sbjct: 361  SALASKATGFPIAKIAAKLAVGYTLDELENDITGGATPASFEPSIDYVVTKIPRFAFEKF 420

Query: 368  AGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFD----PKVSLDDPEALTK 423
             GA   LTT MKSVGEVMAIGRT  ESLQKALRGLE G TG D    P    D+ +    
Sbjct: 421  PGAEPTLTTAMKSVGEVMAIGRTFAESLQKALRGLETGLTGLDEIEVPDFD-DNGDGRNA 479

Query: 424  IRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEVGITG 483
            IR  L     DR+  +A A R G+S   V     ID WF+ Q + +V +E ++ E G+  
Sbjct: 480  IRAALGTPTPDRLRMVAQALRLGMSEAEVHEACKIDPWFIAQFKAIVDMEARIREHGLPA 539

Query: 484  LNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATDTAYM 543
             +A+ LR LK  GF+DARLA L G R  E+ +LR+  ++ PVYKR+DTCAAEFA+ TAYM
Sbjct: 540  -DAENLRMLKAMGFSDARLATLTGKRPKEVAELRNALNVRPVYKRIDTCAAEFASPTAYM 598

Query: 544  YSTYE------EECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETI 597
            YSTYE         EA  S DR+K+++LGGGPNRIGQGIEFDYCC HA+ AL++ GYE I
Sbjct: 599  YSTYETPFVGAARSEAQVS-DRKKVVILGGGPNRIGQGIEFDYCCCHAAFALKDAGYEAI 657

Query: 598  MVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPK----GVIVQYGGQTPLKLARA 653
            M+NCNPETVSTDYDTSDRLYFEP+T EDV+EI+R E+      GVIVQ+GGQTPLKLA A
Sbjct: 658  MINCNPETVSTDYDTSDRLYFEPLTAEDVIEIMRAEQENGTLHGVIVQFGGQTPLKLAEA 717

Query: 654  LEAAGVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYPLV 713
            LE  G+P++GT+PDAID AEDR+RFQ  + +L L QP N    ++E A   A EIG+PLV
Sbjct: 718  LEKNGIPILGTAPDAIDLAEDRDRFQKLLMKLDLNQPNNGIAYSVEQARLVAGEIGFPLV 777

Query: 714  VRPSYVLGGRAMEIVYDEADLRRYFQTAV---------------------SVSNDAPVLL 752
            VRPSYVLGGRAM+I++ E+ L+ Y    V                     ++    P+L 
Sbjct: 778  VRPSYVLGGRAMQIIHSESMLQSYLLDTVPGLVPEDIKQRYPNDKTGQINTLLGKNPLLF 837

Query: 753  DHFLDDAVEVDVDAICDGEMVLIGGIMEHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQ 812
            D +L +A+EVDVD +CDG+ V + GIMEHIE+AG+HSGDSACSLP ++L  ++ D + +Q
Sbjct: 838  DSYLTNAIEVDVDCLCDGKDVFVSGIMEHIEEAGIHSGDSACSLPVHSLGTDMVDELERQ 897

Query: 813  VQKLAFELQVRGLMNVQFAVKNNEVYLIEVNPRAARTVPFVSKATGVPLAKVAARVMAGK 872
               LA  L V GLMNVQFA+K+  +Y++EVNPRA+RTVPFV+K  G P+AK+AARVMAG+
Sbjct: 898  TGALARALNVGGLMNVQFAIKDGTIYVLEVNPRASRTVPFVAKTIGAPIAKIAARVMAGE 957

Query: 873  SLAEQGVTKEVIP-----PYYSVKEVVLPFNKFPGVDPLLGPEMRSTGEVMGVGRTFAEA 927
             L E        P      + +VKE V PF +FPGVD LLGPEMRSTGEV+G+   +A A
Sbjct: 958  MLDEAIAAYGKKPNPRNLKHIAVKEAVFPFARFPGVDTLLGPEMRSTGEVIGLDTDYALA 1017

Query: 928  FAKAQLGSNSTMKKHGRALLSVREGDKERVVDLAAKLLKQGFELDATHGTAIVLGEAGIN 987
            FAK+QLG+   + + G   +SVR+ DKERV+     L   GF++ AT GTA  LGE GI 
Sbjct: 1018 FAKSQLGAGVDLPRDGTVFVSVRDEDKERVLPAIRILSDIGFKVMATGGTARFLGEQGIV 1077

Query: 988  PRLVNKVHEGRPHIQDRIKNGEYTYIINTTSGRRAIEDSRVIRRSALQYKVHYDTTLNGG 1047
               +NKV EGRPH++D I+N +   +INTT G +AI DS+ +RR+ L  KV Y TT+ G 
Sbjct: 1078 ATKINKVLEGRPHVEDAIRNRQVQLVINTTDGNKAISDSKSLRRATLMQKVPYYTTMAGA 1137

Query: 1048 FATAMALNA 1056
             A A+A+ A
Sbjct: 1138 EAAALAIKA 1146


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: 3267
Number of extensions: 162
Number of successful extensions: 20
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 5
Number of HSP's successfully gapped: 4
Length of query: 1073
Length of database: 1163
Length adjustment: 46
Effective length of query: 1027
Effective length of database: 1117
Effective search space:  1147159
Effective search space used:  1147159
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 SMc01215 SMc01215 (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.30273.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 1457.0   0.0          0 1205.9   0.0    2.5  2  lcl|FitnessBrowser__Smeli:SMc01215  SMc01215 carbamoyl phosphate syn


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc01215  SMc01215 carbamoyl phosphate synthase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  248.2   0.0   6.7e-78   6.7e-78       1     152 [.       2     153 ..       2     163 .. 0.97
   2 ! 1205.9   0.0         0         0     144    1051 ..     198    1143 ..     177    1144 .. 0.95

  Alignments for each domain:
  == domain 1  score: 248.2 bits;  conditional E-value: 6.7e-78
                           TIGR01369   1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePltveavek 75 
                                         pkr+dik++l+iG+GpivigqA+EFDYsG+qa+kalkeeg++v+Lvnsn+At+mtd+ lad++Y+eP+t+e+v+k
  lcl|FitnessBrowser__Smeli:SMc01215   2 PKRQDIKSILIIGAGPIVIGQACEFDYSGTQACKALKEEGYRVILVNSNPATIMTDPGLADATYVEPITPEVVAK 76 
                                         689************************************************************************ PP

                           TIGR01369  76 iiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealkeineevakseives 150
                                         ii kErpDa+l+t+GGqtaLn a++l+++GvL++y+v+++G+k eai+kaedR +F+ea+++i++e++ks+ ++ 
  lcl|FitnessBrowser__Smeli:SMc01215  77 IIAKERPDALLPTMGGQTALNTALSLRRMGVLDRYNVEMIGAKPEAIDKAEDRALFREAMAHIGLETPKSRLANA 151
                                         **********************************************************************99987 PP

                           TIGR01369 151 ve 152
                                         ++
  lcl|FitnessBrowser__Smeli:SMc01215 152 TD 153
                                         65 PP

  == domain 2  score: 1205.9 bits;  conditional E-value: 0
                           TIGR01369  144 kseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikqvlvekslagwkEiE 216 
                                          ++ + + ++ a +a +++g+P i+R++ftlgGtG+gia+n++e+ e+v ++l+asp+++vl+e+s+ gwkE+E
  lcl|FitnessBrowser__Smeli:SMc01215  198 QRYVNHAMAIAAQALDDVGLPAIIRPSFTLGGTGGGIAYNRSEFFEIVGSGLDASPTTEVLIEESVLGWKEYE 270 
                                          5667788999*************************************************************** PP

                           TIGR01369  217 yEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslkiirelgvege.cnvqfaldP 288 
                                          +EvvRD++dncii+c+iEn+Dp+GvHtGdsi+vaP+ tLtdkeyq++R+as++++re+gve++ +nvqfa++P
  lcl|FitnessBrowser__Smeli:SMc01215  271 MEVVRDKADNCIIICSIENIDPMGVHTGDSITVAPALTLTDKEYQIMRNASIAVLREIGVETGgSNVQFAVNP 343 
                                          *************************************************************988********* PP

                           TIGR01369  289 eskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelkndvtk.etvAsfEPslDYvvvkiPrwd 360 
                                          e+ r+vviE+npRvsRssALAskAtG+PiAk+aaklavGy+Ldel+nd+t+  t+AsfEPs+DYvv+kiPr++
  lcl|FitnessBrowser__Smeli:SMc01215  344 ENGRLVVIEMNPRVSRSSALASKATGFPIAKIAAKLAVGYTLDELENDITGgATPASFEPSIDYVVTKIPRFA 416 
                                          **************************************************878******************** PP

                           TIGR01369  361 ldkfekvdrklgtqmksvGEvmaigrtfeealqkalrsleekllglklkek.....eaesdeeleealkkpnd 428 
                                          ++kf +++ +l+t mksvGEvmaigrtf e+lqkalr le++l+gl++ e      +   +++++ al +p++
  lcl|FitnessBrowser__Smeli:SMc01215  417 FEKFPGAEPTLTTAMKSVGEVMAIGRTFAESLQKALRGLETGLTGLDEIEVpdfddNGDGRNAIRAALGTPTP 489 
                                          *********************************************655433100103334567788999**** PP

                           TIGR01369  429 rRlfaiaealrrgvsveevyeltkidrffleklkklvelekeleeeklkelkkellkkakklGfsdeqiaklv 501 
                                          +Rl ++a+alr g+s  ev+e++kid +f+ ++k +v++e +++e+ l   ++e+l+ +k++Gfsd+++a+l+
  lcl|FitnessBrowser__Smeli:SMc01215  490 DRLRMVAQALRLGMSEAEVHEACKIDPWFIAQFKAIVDMEARIREHGLP-ADAENLRMLKAMGFSDARLATLT 561 
                                          ********************************************88887.99********************* PP

                           TIGR01369  502 kvseaevrklrkelgivpvvkrvDtvaaEfeaktpYlYstyeee.....kddvevtekkkvlvlGsGpiRigq 569 
                                          +++ +ev +lr++l++ pv+kr+Dt+aaEf + t+Y+Ystye+      + +++v+++kkv++lG+Gp+Rigq
  lcl|FitnessBrowser__Smeli:SMc01215  562 GKRPKEVAELRNALNVRPVYKRIDTCAAEFASPTAYMYSTYETPfvgaaRSEAQVSDRKKVVILGGGPNRIGQ 634 
                                          *****************************************9877777799********************** PP

                           TIGR01369  570 gvEFDycavhavlalreagyktilinynPEtvstDydiadrLyFeeltvedvldiiekek....vegvivqlg 638 
                                          g+EFDyc+ ha+ al++agy++i+in+nPEtvstDyd++drLyFe+lt edv++i++ e+     +gvivq+g
  lcl|FitnessBrowser__Smeli:SMc01215  635 GIEFDYCCCHAAFALKDAGYEAIMINCNPETVSTDYDTSDRLYFEPLTAEDVIEIMRAEQengtLHGVIVQFG 707 
                                          ********************************************************99873333578****** PP

                           TIGR01369  639 GqtalnlakeleeagvkilGtsaesidraEdRekFsklldelgikqpkgkeatsveeakeiakeigyPvlvRp 711 
                                          Gqt+l+la++le++g++ilGt +++id aEdR++F+kll +l+++qp++ +a sve+a+ +a eig+P++vRp
  lcl|FitnessBrowser__Smeli:SMc01215  708 GQTPLKLAEALEKNGIPILGTAPDAIDLAEDRDRFQKLLMKLDLNQPNNGIAYSVEQARLVAGEIGFPLVVRP 780 
                                          ************************************************************************* PP

                           TIGR01369  712 syvlgGrameiveneeeleryle.....................eavevskekPvlidkyledavEvdvDava 763 
                                          syvlgGram+i+++e  l++yl                      +++++  ++P+l d yl++a+EvdvD ++
  lcl|FitnessBrowser__Smeli:SMc01215  781 SYVLGGRAMQIIHSESMLQSYLLdtvpglvpedikqrypndktgQINTLLGKNPLLFDSYLTNAIEVDVDCLC 853 
                                          *********************9767888888888888887766656677789********************* PP

                           TIGR01369  764 dgeevliagileHiEeaGvHsGDstlvlppqklseevkkkikeivkkiakelkvkGllniqfvvkdeevyviE 836 
                                          dg++v++ gi+eHiEeaG+HsGDs+++lp ++l +++++++++++ ++a++l+v Gl+n+qf++kd+++yv+E
  lcl|FitnessBrowser__Smeli:SMc01215  854 DGKDVFVSGIMEHIEEAGIHSGDSACSLPVHSLGTDMVDELERQTGALARALNVGGLMNVQFAIKDGTIYVLE 926 
                                          ************************************************************************* PP

                           TIGR01369  837 vnvRasRtvPfvskalgvplvklavkvllgkkleelekgvkkek...ksklvavkaavfsfsklagvdvvlgp 906 
                                          vn+RasRtvPfv+k++g p++k+a++v++g+ l e+  +  k++   + k++avk+avf+f+++ gvd +lgp
  lcl|FitnessBrowser__Smeli:SMc01215  927 VNPRASRTVPFVAKTIGAPIAKIAARVMAGEMLDEAIAAYGKKPnprNLKHIAVKEAVFPFARFPGVDTLLGP 999 
                                          **********************************98876666541115789********************** PP

                           TIGR01369  907 emkstGEvmgigrdleeallkallaskakikkkgsvllsvkdkdkeellelakklaekglkvyategtakvle 979 
                                          em+stGEv+g+++d + a++k++l ++  ++++g+v++sv+d+dke++l++++ l ++g+kv+at gta++l 
  lcl|FitnessBrowser__Smeli:SMc01215 1000 EMRSTGEVIGLDTDYALAFAKSQLGAGVDLPRDGTVFVSVRDEDKERVLPAIRILSDIGFKVMATGGTARFLG 1072
                                          ************************************************************************* PP

                           TIGR01369  980 eagikaevvlkvseeaekilellkeeeielvinltskkkkaaekgykirreaveykvplvteletaeallea 1051
                                          e+gi a++++kv e ++++ +++++++++lvin+t+ ++ka ++++++rr+++++kvp+ t++++aea++ a
  lcl|FitnessBrowser__Smeli:SMc01215 1073 EQGIVATKINKVLEGRPHVEDAIRNRQVQLVINTTD-GNKAISDSKSLRRATLMQKVPYYTTMAGAEAAALA 1143
                                          *********************************998.88899999*******************99988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1052 nodes)
Target sequences:                          1  (1163 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: 0.18u 0.03s 00:00:00.21 Elapsed: 00:00:00.20
# Mc/sec: 5.88
//
[ok]

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