Alignments for a candidate for carB in Rhodospirillum rubrum ATCC 11170

GapMind for Amino acid biosynthesis

Alignments for a candidate for carB in Rhodospirillum rubrum ATCC 11170

Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate WP_011390636.1 RRU_RS14890 carbamoyl-phosphate synthase large subunit

Query= BRENDA::P00968
         (1073 letters)



>NCBI__GCF_000013085.1:WP_011390636.1
          Length = 1082

 Score = 1292 bits (3344), Expect = 0.0
 Identities = 675/1072 (62%), Positives = 819/1072 (76%), Gaps = 24/1072 (2%)

Query: 1    MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
            MPKRTDIKSILI+GAGPIVIGQACEFDYSGAQACKALR EGYRVILVNSNPATIMTDPE 
Sbjct: 1    MPKRTDIKSILIIGAGPIVIGQACEFDYSGAQACKALRAEGYRVILVNSNPATIMTDPET 60

Query: 61   ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
            ADATYIEPI  E+V  IIE+ERPDA+LPTMGGQTALN A+ L  +GVL ++GV MI A  
Sbjct: 61   ADATYIEPITPEIVEAIIERERPDALLPTMGGQTALNTAMALADRGVLTKYGVEMIAANK 120

Query: 121  DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180
            + I KAEDR  F  AM+KIGL+  RS + H++EE+     ++G P IIRPSFT+GG GGG
Sbjct: 121  EVIAKAEDRLLFRDAMRKIGLDCPRSALVHSIEESRQALEEIGLPVIIRPSFTLGGQGGG 180

Query: 181  IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM 240
            +A+NREE++ I A GL  SP +++L++ES++GWKEYEMEVVRD+ DNCIIVCSIEN D M
Sbjct: 181  MAFNREEYDRIVASGLAASPVRQILVEESVLGWKEYEMEVVRDRADNCIIVCSIENIDPM 240

Query: 241  GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM 300
            G+HTGDSITVAPA TLTDKEYQ+MRNAS+A LREIGVETGGSNVQFAVNPK+GRL+VIEM
Sbjct: 241  GVHTGDSITVAPALTLTDKEYQVMRNASIACLREIGVETGGSNVQFAVNPKDGRLVVIEM 300

Query: 301  NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP 360
            NPRVSRSSALASKATGFPIAK+AAKLAVGYTLDEL NDIT G TPASFEP+IDYVVTK+P
Sbjct: 301  NPRVSRSSALASKATGFPIAKIAAKLAVGYTLDELSNDIT-GVTPASFEPTIDYVVTKLP 359

Query: 361  RFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDP-----KVSL 415
            RF FEKF      L++ MKSVGE MAIGRT +ESLQK LR LE+G  G D          
Sbjct: 360  RFTFEKFPDTEALLSSSMKSVGEAMAIGRTFKESLQKGLRSLEIGLDGLDEVEIPGSAGQ 419

Query: 416  DDPEALTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEK 475
            D  +A   IR  L  A  DRI  IA A R G +V+ V  +   D WFL QI+E+V  E +
Sbjct: 420  DGKDA---IRAALSKARPDRILIIAQALRQGFTVEEVRAICYYDPWFLEQIKEIVDEERR 476

Query: 476  VAEVGITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAE 535
            + E G+ G +A  L ++K+ GF+DARLAKL G    E+   R   ++HPVYKR+DTCAAE
Sbjct: 477  LRENGLPG-DAVSLHRVKKMGFSDARLAKLTGKTVTEVSFRRQVLNVHPVYKRIDTCAAE 535

Query: 536  FATDTAYMYSTYE------EECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLAL 589
            FA+ T YMYS YE       ECEA  S DR KI++LGGGPNRIGQGIEFDYCCVHA+ AL
Sbjct: 536  FASRTPYMYSCYEGDGLTPAECEAEVS-DRTKIIILGGGPNRIGQGIEFDYCCVHAAYAL 594

Query: 590  REDGYETIMVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGV----IVQYGGQ 645
             + G+ETIMVNCNPETVSTDYDTSDRLYFEP+T+EDV+E+ R E+ +G     IVQYGGQ
Sbjct: 595  SDAGFETIMVNCNPETVSTDYDTSDRLYFEPLTIEDVVELARKEQARGTLLGCIVQYGGQ 654

Query: 646  TPLKLARALEAAGVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKA 705
            TPLKLAR LEAAG+PV+GTSPDAID AEDR+RFQ  + +L L+QP N T  ++E A   A
Sbjct: 655  TPLKLARGLEAAGIPVLGTSPDAIDLAEDRDRFQKLIAKLALRQPRNGTALSVEQARAIA 714

Query: 706  KEIGYPLVVRPSYVLGGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVD 765
              +GYP+V+RPSYVLGGRAM+IV+DEA L  Y   AV VS D PVL+D++L  A+EVDVD
Sbjct: 715  TRVGYPVVIRPSYVLGGRAMQIVHDEAQLNDYMVNAVKVSGDDPVLIDNYLSGAIEVDVD 774

Query: 766  AICDGEMVLIGGIMEHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGL 825
            AI DGE   I GIM+HIE+AG+HSGDSACSLP Y+L +     + +Q + LA  L VRGL
Sbjct: 775  AIADGETTHIAGIMQHIEEAGIHSGDSACSLPPYSLDEATIAELTKQTEALAKGLNVRGL 834

Query: 826  MNVQFAVKNNEVYLIEVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQG-VTKEVI 884
            MN+QFA+K+ ++Y++EVNPRA+RTVPFV+KATGV +AK+AARVMAG+SLA  G VTK + 
Sbjct: 835  MNIQFAIKDGDIYILEVNPRASRTVPFVAKATGVAVAKIAARVMAGESLASFGLVTKRL- 893

Query: 885  PPYYSVKEVVLPFNKFPGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGR 944
              + +VKE V PF +FPGVD +LGPEM+STGEVMG+  TFA AFAK+QLG+  T+ + G 
Sbjct: 894  -AHVAVKEAVFPFARFPGVDIVLGPEMKSTGEVMGIDTTFARAFAKSQLGAGVTLPEGGT 952

Query: 945  ALLSVREGDKERVVDLAAKLLKQGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDR 1004
            A +SVR+GDK  ++ +A +L + GF L AT GTA +L E G++  ++NKV EGRPH  D 
Sbjct: 953  AFISVRDGDKAAIMPIARELTELGFRLVATRGTAALLAENGLSVEVINKVLEGRPHCVDA 1012

Query: 1005 IKNGEYTYIINTTSGRRAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNA 1056
            + +G+   + NTT G ++ +DS  IR +AL   + + TT+ G  A   A+ A
Sbjct: 1013 MISGDIHLVFNTTEGIQSQKDSFDIRHTALMRNIPHYTTVAGATAAVKAMTA 1064


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: 3102
Number of extensions: 153
Number of successful extensions: 17
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: 1073
Length of database: 1082
Length adjustment: 46
Effective length of query: 1027
Effective length of database: 1036
Effective search space:  1063972
Effective search space used:  1063972
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 WP_011390636.1 RRU_RS14890 (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.2704099.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 1494.8   0.0          0 1494.6   0.0    1.0  1  NCBI__GCF_000013085.1:WP_011390636.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000013085.1:WP_011390636.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1494.6   0.0         0         0       1    1052 []       2    1062 ..       2    1062 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1494.6 bits;  conditional E-value: 0
                             TIGR01369    1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePltve 71  
                                            pkr+dik++l+iG+GpivigqA+EFDYsG+qa+kal+ eg++v+Lvnsn+At+mtd+e ad++YieP+t+e
  NCBI__GCF_000013085.1:WP_011390636.1    2 PKRTDIKSILIIGAGPIVIGQACEFDYSGAQACKALRAEGYRVILVNSNPATIMTDPETADATYIEPITPE 72  
                                            689******************************************************************** PP

                             TIGR01369   72 avekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealkeineev 142 
                                            +ve iie+ErpDa+l+t+GGqtaLn a+ l ++GvL kygv+++ ++ e+i+kaedR +F++a+++i+++ 
  NCBI__GCF_000013085.1:WP_011390636.1   73 IVEAIIERERPDALLPTMGGQTALNTAMALADRGVLTKYGVEMIAANKEVIAKAEDRLLFRDAMRKIGLDC 143 
                                            *********************************************************************** PP

                             TIGR01369  143 akseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikqvlvekslagwk 213 
                                            ++s+ v+s+ee+ +a eeig+Pvi+R++ftlgG+G+g+a n+ee  ++v+++l+asp++q+lve+s+ gwk
  NCBI__GCF_000013085.1:WP_011390636.1  144 PRSALVHSIEESRQALEEIGLPVIIRPSFTLGGQGGGMAFNREEYDRIVASGLAASPVRQILVEESVLGWK 214 
                                            *********************************************************************** PP

                             TIGR01369  214 EiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslkiirelgvege.cnvq 283 
                                            E+E+EvvRD++dnciivc+iEn+Dp+GvHtGdsi+vaP+ tLtdkeyq +R+as++ +re+gve++ +nvq
  NCBI__GCF_000013085.1:WP_011390636.1  215 EYEMEVVRDRADNCIIVCSIENIDPMGVHTGDSITVAPALTLTDKEYQVMRNASIACLREIGVETGgSNVQ 285 
                                            ****************************************************************988**** PP

                             TIGR01369  284 faldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelkndvtketvAsfEPslDYvvv 354 
                                            fa++P++ r+vviE+npRvsRssALAskAtG+PiAk+aaklavGy+Ldel+nd+t+ t+AsfEP++DYvv+
  NCBI__GCF_000013085.1:WP_011390636.1  286 FAVNPKDGRLVVIEMNPRVSRSSALASKATGFPIAKIAAKLAVGYTLDELSNDITGVTPASFEPTIDYVVT 356 
                                            *********************************************************************** PP

                             TIGR01369  355 kiPrwdldkfekvdrklgtqmksvGEvmaigrtfeealqkalrsleekllg...lklkeke.aesdeelee 421 
                                            k+Pr+ ++kf  ++  l+++mksvGE maigrtf+e+lqk+lrsle++l g   ++++ ++ +  +++++ 
  NCBI__GCF_000013085.1:WP_011390636.1  357 KLPRFTFEKFPDTEALLSSSMKSVGEAMAIGRTFKESLQKGLRSLEIGLDGldeVEIPGSAgQDGKDAIRA 427 
                                            **************************************************944444444441344566788 PP

                             TIGR01369  422 alkkpndrRlfaiaealrrgvsveevyeltkidrffleklkklvelekeleeeklkelkkellkkakklGf 492 
                                            al k+ ++R+++ia+alr+g++veev  ++ +d +fle++k++v+ e++l+e+ l   ++ +l+++kk+Gf
  NCBI__GCF_000013085.1:WP_011390636.1  428 ALSKARPDRILIIAQALRQGFTVEEVRAICYYDPWFLEQIKEIVDEERRLRENGLP-GDAVSLHRVKKMGF 497 
                                            999***********************************************987777.89999********* PP

                             TIGR01369  493 sdeqiaklvkvseaevrklrkelgivpvvkrvDtvaaEfeaktpYlYstyeee.....kddvevtekkkvl 558 
                                            sd+++akl++++ +ev   r+ l+++pv+kr+Dt+aaEf ++tpY+Ys ye++     + ++ev+++ k++
  NCBI__GCF_000013085.1:WP_011390636.1  498 SDARLAKLTGKTVTEVSFRRQVLNVHPVYKRIDTCAAEFASRTPYMYSCYEGDgltpaECEAEVSDRTKII 568 
                                            ***************************************************9988877779999999**** PP

                             TIGR01369  559 vlGsGpiRigqgvEFDycavhavlalreagyktilinynPEtvstDydiadrLyFeeltvedvldiiekek 629 
                                            +lG+Gp+Rigqg+EFDyc+vha+ al++ag++ti++n+nPEtvstDyd++drLyFe+lt+edv+++ +ke+
  NCBI__GCF_000013085.1:WP_011390636.1  569 ILGGGPNRIGQGIEFDYCCVHAAYALSDAGFETIMVNCNPETVSTDYDTSDRLYFEPLTIEDVVELARKEQ 639 
                                            *********************************************************************** PP

                             TIGR01369  630 ve....gvivqlgGqtalnlakeleeagvkilGtsaesidraEdRekFsklldelgikqpkgkeatsveea 696 
                                             +    g+ivq+gGqt+l+la+ le+ag+++lGts+++id aEdR++F+kl+ +l + qp++ +a sve+a
  NCBI__GCF_000013085.1:WP_011390636.1  640 ARgtllGCIVQYGGQTPLKLARGLEAAGIPVLGTSPDAIDLAEDRDRFQKLIAKLALRQPRNGTALSVEQA 710 
                                            98333358*************************************************************** PP

                             TIGR01369  697 keiakeigyPvlvRpsyvlgGrameiveneeeleryleeavevskekPvlidkyledavEvdvDavadgee 767 
                                            + ia+++gyPv++RpsyvlgGram+iv++e++l++y+ +av+vs + Pvlid+yl+ a+EvdvDa+adge+
  NCBI__GCF_000013085.1:WP_011390636.1  711 RAIATRVGYPVVIRPSYVLGGRAMQIVHDEAQLNDYMVNAVKVSGDDPVLIDNYLSGAIEVDVDAIADGET 781 
                                            *********************************************************************** PP

                             TIGR01369  768 vliagileHiEeaGvHsGDstlvlppqklseevkkkikeivkkiakelkvkGllniqfvvkdeevyviEvn 838 
                                              iagi++HiEeaG+HsGDs+++lpp +l+e +  +++++++++ak l+v+Gl+niqf++kd+++y++Evn
  NCBI__GCF_000013085.1:WP_011390636.1  782 THIAGIMQHIEEAGIHSGDSACSLPPYSLDEATIAELTKQTEALAKGLNVRGLMNIQFAIKDGDIYILEVN 852 
                                            *********************************************************************** PP

                             TIGR01369  839 vRasRtvPfvskalgvplvklavkvllgkkleelekgvkkekksklvavkaavfsfsklagvdvvlgpemk 909 
                                            +RasRtvPfv+ka+gv ++k+a++v++g++l++ +     +k+  +vavk+avf+f+++ gvd+vlgpemk
  NCBI__GCF_000013085.1:WP_011390636.1  853 PRASRTVPFVAKATGVAVAKIAARVMAGESLASFGL---VTKRLAHVAVKEAVFPFARFPGVDIVLGPEMK 920 
                                            *********************************886...666778************************** PP

                             TIGR01369  910 stGEvmgigrdleeallkallaskakikkkgsvllsvkdkdkeellelakklaekglkvyategtakvlee 980 
                                            stGEvmgi++++++a++k++l ++ ++++ g++++sv+d dk +++++a++l+e+g++++at+gta+ l+e
  NCBI__GCF_000013085.1:WP_011390636.1  921 STGEVMGIDTTFARAFAKSQLGAGVTLPEGGTAFISVRDGDKAAIMPIARELTELGFRLVATRGTAALLAE 991 
                                            *********************************************************************** PP

                             TIGR01369  981 agikaevvlkvseeaekilellkeeeielvinltskkkkaaekgykirreaveykvplvteletaeallea 1051
                                            +g ++ev++kv e ++++++++ +++i+lv+n+t+ + +++++++ ir++a+++++p+ t++++a+a+++a
  NCBI__GCF_000013085.1:WP_011390636.1  992 NGLSVEVINKVLEGRPHCVDAMISGDIHLVFNTTE-GIQSQKDSFDIRHTALMRNIPHYTTVAGATAAVKA 1061
                                            ********************************997.888999***********************999988 PP

                             TIGR01369 1052 l 1052
                                            +
  NCBI__GCF_000013085.1:WP_011390636.1 1062 M 1062
                                            5 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1052 nodes)
Target sequences:                          1  (1082 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 0.08s 00:00:00.12 Elapsed: 00:00:00.11
# Mc/sec: 9.84
//
[ok]

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