Alignments for a candidate for carB in Mycolicibacterium vanbaalenii PYR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for carB in Mycolicibacterium vanbaalenii PYR-1

Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate WP_011779880.1 MVAN_RS13380 carbamoyl phosphate synthase large subunit

Query= BRENDA::P00968
         (1073 letters)



>NCBI__GCF_000015305.1:WP_011779880.1
          Length = 1112

 Score = 1064 bits (2752), Expect = 0.0
 Identities = 582/1123 (51%), Positives = 750/1123 (66%), Gaps = 64/1123 (5%)

Query: 1    MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
            MP+R D+  +L++G+GPI+IGQA EFDYSG QAC+ LR EG +V L+NSNPATIMTDPE 
Sbjct: 1    MPRRPDLNHVLVIGSGPILIGQAAEFDYSGTQACRVLRAEGLQVTLINSNPATIMTDPEY 60

Query: 61   ADATYIEPIHWEVVRKIIEKE-----RPDAVLPTMGGQTALNCALELERQGVLEEFGVTM 115
            AD TY+EPI  E V K+I ++     + DA+L T+GGQTALN A++L   G LE +GV +
Sbjct: 61   ADHTYVEPITAEFVEKVIAQQAERGNKIDALLATLGGQTALNTAVKLSENGALERYGVEL 120

Query: 116  IGATADAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMG 175
            IGA  +AI + EDR++F   + K+G E+ARS +  TM+E     AD+G P ++RPSFTMG
Sbjct: 121  IGADFEAIQRGEDRQKFKDIVTKVGGESARSRVCFTMDEVRDTVADLGLPVVVRPSFTMG 180

Query: 176  GSGGGIAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIE 235
            G G G+AY+ E+ E +   GL  SP+  +LI+ES+ GWKEYE+E++RD +DN ++VCSIE
Sbjct: 181  GLGSGMAYSAEDVERMAGDGLAASPSANVLIEESIYGWKEYELELMRDGHDNVVVVCSIE 240

Query: 236  NFDAMGIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRL 295
            NFD MG+HTGDS+TVAPA TLTD+EYQ MR   + +LRE+GV+TGG N+QFAVNPK+GRL
Sbjct: 241  NFDPMGVHTGDSVTVAPAMTLTDREYQTMRTLGIEILREVGVDTGGCNIQFAVNPKDGRL 300

Query: 296  IVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYV 355
            IVIEMNPRVSRSSALASKATGFPIAK+AAKLA+GYTLDE++NDIT   TPA FEP++DYV
Sbjct: 301  IVIEMNPRVSRSSALASKATGFPIAKIAAKLAIGYTLDEIVNDIT-KETPACFEPTLDYV 359

Query: 356  VTKIPRFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGF----DP 411
            V K PRF FEKF GA+  LTT MKSVGE M++GR   E+L K +R LE G  GF    DP
Sbjct: 360  VVKAPRFAFEKFPGADGTLTTTMKSVGEAMSLGRNFIEALGKVMRSLETGRAGFWTGPDP 419

Query: 412  KVSLDDPEALTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVR 471
            + S+D  E LT+    L  A   R++ I  A R G +V+ V   + +D WF+ QI  LV 
Sbjct: 420  EGSVD--EVLTR----LHTATDGRLYDIEYALRLGATVEQVAVASGVDPWFVEQIGRLVA 473

Query: 472  LEEKVAEVGITGLNADFLRQLKRKGFADARLA----KLAGVREAEIRKLRDQYDLHPVYK 527
            L  ++ +  + G   + LR+ K  G +D ++A    +LAG  E  +R LR +  +HPV+K
Sbjct: 474  LRAELIDAPVLG--EELLRRSKHNGLSDRQIAALRPELAG--EMGVRVLRQRLGIHPVFK 529

Query: 528  RVDTCAAEFATDTAYMYSTYE----EECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCV 583
             VDTCAAEF   T Y YS+YE     E E  P  +R K+++LG GPNRIGQGIEFDY CV
Sbjct: 530  TVDTCAAEFEARTPYHYSSYELDPSAETEVAPQAERPKVLILGSGPNRIGQGIEFDYSCV 589

Query: 584  HASLALREDGYETIMVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPK------- 636
            HA+  L E G+ET+M+NCNPETVSTDYDT+DRLYFEP+T EDVLEI   E+         
Sbjct: 590  HAATTLTEAGFETVMINCNPETVSTDYDTADRLYFEPLTFEDVLEIYYAEQASGEGGPGV 649

Query: 637  -GVIVQYGGQTPLKLARALEAAGVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATV 695
             GVIVQ GGQTPL LA  LE AGVP++GT P+AID AEDR  F   + R  L  P     
Sbjct: 650  VGVIVQLGGQTPLGLAERLEKAGVPIVGTLPEAIDLAEDRGEFGEVLRRAGLPAPRFGMA 709

Query: 696  TAIEMAVEKAKEIGYPLVVRPSYVLGGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHF 755
            T+ + A   A EIGYP++VRPSYVLGGR MEIVYDE  L  Y   A  +S + PVL+D F
Sbjct: 710  TSFDQARRIAAEIGYPVLVRPSYVLGGRGMEIVYDEETLEGYITRATELSPEHPVLVDRF 769

Query: 756  LDDAVEVDVDAICDGEMVLIGGIMEHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQK 815
            L+DA+E+DVDA+CDG  V IGG+MEHIE+AG+HSGDSAC+LP  TL +   + +R+  + 
Sbjct: 770  LEDAIEIDVDALCDGTEVYIGGVMEHIEEAGIHSGDSACALPPVTLGRSDIEAVRRATEA 829

Query: 816  LAFELQVRGLMNVQFAVKNNEVYLIEVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLA 875
            +AF + V GL+NVQ+A+K++ +Y++E NPRA+RTVPFVSKAT VPLAK  AR+M G ++A
Sbjct: 830  IAFGIGVVGLLNVQYALKDDVLYVLEANPRASRTVPFVSKATAVPLAKACARIMLGATIA 889

Query: 876  ---EQG---------VTKEVIPPYYSVKEVVLPFNKF-----PGVDPLLGPEMRSTGEVM 918
               E+G         VT    P   +VKE VLPF++F       +D LLGPEM+STGEVM
Sbjct: 890  QLREEGVLASTGDGAVTARNAP--VAVKEAVLPFHRFRKADGSQIDSLLGPEMKSTGEVM 947

Query: 919  GVGRTFAEAFAKAQLGSNSTMKKHGRALLSVREGDKERVVDLAAKLLKQGFELDATHGTA 978
            G+   F  AFAK+Q  +  ++   G   +SV   DK  +V    +L   GF + AT GTA
Sbjct: 948  GIAADFGSAFAKSQTAAYGSLPAQGTVFVSVANRDKRSLVFPVKRLADLGFRVLATEGTA 1007

Query: 979  IVLGEAGINPRLVNK----VHEGRPHIQ--DRIKNGEYTYIINTTSGRRAIE-DSRVIRR 1031
             +L   GI    V K      EG P +   D IK G    +INT  G      D   IR 
Sbjct: 1008 EMLRRNGIPCEEVRKHFQEFSEGLPQMSAVDAIKAGHVDMVINTPYGNSGPRIDGYEIRS 1067

Query: 1032 SALQYKVHYDTTLNGGFATAMALNADATEK--VISVQEMHAQI 1072
            +A+   +   TT+ G  A    + A       V S+QE+H+ +
Sbjct: 1068 AAVSMNIPCVTTVQGASAAVQGIEAGIRGDIGVRSLQELHSAL 1110


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: 3015
Number of extensions: 137
Number of successful extensions: 19
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: 1112
Length adjustment: 46
Effective length of query: 1027
Effective length of database: 1066
Effective search space:  1094782
Effective search space used:  1094782
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_011779880.1 MVAN_RS13380 (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.13445.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 1375.2   0.0          0 1375.1   0.0    1.0  1  lcl|NCBI__GCF_000015305.1:WP_011779880.1  MVAN_RS13380 carbamoyl phosphate


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015305.1:WP_011779880.1  MVAN_RS13380 carbamoyl phosphate synthase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1375.1   0.0         0         0       2    1050 ..       3    1088 ..       2    1090 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1375.1 bits;  conditional E-value: 0
                                 TIGR01369    2 kredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePl 68  
                                                +r d+++vlviGsGpi igqAaEFDYsG+qa++ l+ eg++v L+nsn+At+mtd+e ad++Y+eP+
  lcl|NCBI__GCF_000015305.1:WP_011779880.1    3 RRPDLNHVLVIGSGPILIGQAAEFDYSGTQACRVLRAEGLQVTLINSNPATIMTDPEYADHTYVEPI 69  
                                                68899************************************************************** PP

                                 TIGR01369   69 tveavekiiek.....ErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRek 130 
                                                t+e+vek+i +     +++Da+l+tlGGqtaLn av+l+e+G Le+ygv+l+G+++eai+++edR+k
  lcl|NCBI__GCF_000015305.1:WP_011779880.1   70 TAEFVEKVIAQqaergNKIDALLATLGGQTALNTAVKLSENGALERYGVELIGADFEAIQRGEDRQK 136 
                                                *********7633223589************************************************ PP

                                 TIGR01369  131 FkealkeineevakseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalka 197 
                                                Fk+ +++++ e a+s+++ +++e  ++++++g+Pv+vR++ft+gG Gsg+a+++e++++++  +l+a
  lcl|NCBI__GCF_000015305.1:WP_011779880.1  137 FKDIVTKVGGESARSRVCFTMDEVRDTVADLGLPVVVRPSFTMGGLGSGMAYSAEDVERMAGDGLAA 203 
                                                ******************************************************************* PP

                                 TIGR01369  198 spikqvlvekslagwkEiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllR 264 
                                                sp  +vl+e+s++gwkE+E+E +RD +dn+++vc+iEn+Dp+GvHtGds++vaP+ tLtd+eyq++R
  lcl|NCBI__GCF_000015305.1:WP_011779880.1  204 SPSANVLIEESIYGWKEYELELMRDGHDNVVVVCSIENFDPMGVHTGDSVTVAPAMTLTDREYQTMR 270 
                                                ******************************************************************* PP

                                 TIGR01369  265 daslkiirelgvege.cnvqfaldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysL 330 
                                                +  ++i+re+gv+++ cn+qfa++P++ r++viE+npRvsRssALAskAtG+PiAk+aakla+Gy+L
  lcl|NCBI__GCF_000015305.1:WP_011779880.1  271 TLGIEILREVGVDTGgCNIQFAVNPKDGRLIVIEMNPRVSRSSALASKATGFPIAKIAAKLAIGYTL 337 
                                                ************9988*************************************************** PP

                                 TIGR01369  331 delkndvtketvAsfEPslDYvvvkiPrwdldkfekvdrklgtqmksvGEvmaigrtfeealqkalr 397 
                                                de+ nd+tket+A+fEP+lDYvvvk Pr++++kf ++d +l+t+mksvGE m++gr+f eal k +r
  lcl|NCBI__GCF_000015305.1:WP_011779880.1  338 DEIVNDITKETPACFEPTLDYVVVKAPRFAFEKFPGADGTLTTTMKSVGEAMSLGRNFIEALGKVMR 404 
                                                ******************************************************************* PP

                                 TIGR01369  398 sleekllglklkekeaesdeeleealkkpndrRlfaiaealrrgvsveevyeltkidrffleklkkl 464 
                                                sle++  g+ +  + + s +e+ ++l++++d Rl+ i  alr g++ve+v  ++ +d +f+e++ +l
  lcl|NCBI__GCF_000015305.1:WP_011779880.1  405 SLETGRAGFWTGPDPEGSVDEVLTRLHTATDGRLYDIEYALRLGATVEQVAVASGVDPWFVEQIGRL 471 
                                                ********99999999999999********************************************* PP

                                 TIGR01369  465 velekeleeeklkelkkellkkakklGfsdeqiaklvk..vseaevrklrkelgivpvvkrvDtvaa 529 
                                                v+l  el    +  l +ell++ k+ G+sd+qia+l      e  vr lr++lgi+pv+k+vDt+aa
  lcl|NCBI__GCF_000015305.1:WP_011779880.1  472 VALRAELI--DAPVLGEELLRRSKHNGLSDRQIAALRPelAGEMGVRVLRQRLGIHPVFKTVDTCAA 536 
                                                ******97..566689******************99872245666********************** PP

                                 TIGR01369  530 EfeaktpYlYstyeee....kddvevtekkkvlvlGsGpiRigqgvEFDycavhavlalreagykti 592 
                                                Efea+tpY+Ys+ye +    ++ +++ e+ kvl+lGsGp+Rigqg+EFDy++vha+++l eag++t+
  lcl|NCBI__GCF_000015305.1:WP_011779880.1  537 EFEARTPYHYSSYELDpsaeTEVAPQAERPKVLILGSGPNRIGQGIEFDYSCVHAATTLTEAGFETV 603 
                                                *************97654423444556679************************************* PP

                                 TIGR01369  593 linynPEtvstDydiadrLyFeeltvedvldiiekek........vegvivqlgGqtalnlakelee 651 
                                                +in+nPEtvstDyd+adrLyFe+lt+edvl+i+  e+        v gvivqlgGqt+l la++le+
  lcl|NCBI__GCF_000015305.1:WP_011779880.1  604 MINCNPETVSTDYDTADRLYFEPLTFEDVLEIYYAEQasgeggpgVVGVIVQLGGQTPLGLAERLEK 670 
                                                **********************************99933333333457******************* PP

                                 TIGR01369  652 agvkilGtsaesidraEdRekFsklldelgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgGr 718 
                                                agv+i+Gt +e+id aEdR +F ++l++ g++ p++ +ats ++a++ia+eigyPvlvRpsyvlgGr
  lcl|NCBI__GCF_000015305.1:WP_011779880.1  671 AGVPIVGTLPEAIDLAEDRGEFGEVLRRAGLPAPRFGMATSFDQARRIAAEIGYPVLVRPSYVLGGR 737 
                                                ******************************************************************* PP

                                 TIGR01369  719 ameiveneeeleryleeavevskekPvlidkyledavEvdvDavadgeevliagileHiEeaGvHsG 785 
                                                +meiv++ee+le y+++a+e+s+e+Pvl+d++leda+E+dvDa++dg+ev+i g++eHiEeaG+HsG
  lcl|NCBI__GCF_000015305.1:WP_011779880.1  738 GMEIVYDEETLEGYITRATELSPEHPVLVDRFLEDAIEIDVDALCDGTEVYIGGVMEHIEEAGIHSG 804 
                                                ******************************************************************* PP

                                 TIGR01369  786 DstlvlppqklseevkkkikeivkkiakelkvkGllniqfvvkdeevyviEvnvRasRtvPfvskal 852 
                                                Ds++ lpp +l ++  +++++++++ia  + v+Glln+q+++kd+ +yv+E+n+RasRtvPfvska+
  lcl|NCBI__GCF_000015305.1:WP_011779880.1  805 DSACALPPVTLGRSDIEAVRRATEAIAFGIGVVGLLNVQYALKDDVLYVLEANPRASRTVPFVSKAT 871 
                                                ******************************************************************* PP

                                 TIGR01369  853 gvplvklavkvllgkkleele.........kgvkkekksklvavkaavfsfsklagv.....dvvlg 905 
                                                 vpl+k  ++++lg+++++l          +g   ++++  vavk+av++f++++++     d +lg
  lcl|NCBI__GCF_000015305.1:WP_011779880.1  872 AVPLAKACARIMLGATIAQLReegvlastgDG-AVTARNAPVAVKEAVLPFHRFRKAdgsqiDSLLG 937 
                                                ******************99887787765422.345566789************87522222689** PP

                                 TIGR01369  906 pemkstGEvmgigrdleeallkallaskakikkkgsvllsvkdkdkeellelakklaekglkvyate 972 
                                                pemkstGEvmgi+ d+ +a++k+++a+   ++ +g+v++sv+++dk++l+  +k+la++g++v+ate
  lcl|NCBI__GCF_000015305.1:WP_011779880.1  938 PEMKSTGEVMGIAADFGSAFAKSQTAAYGSLPAQGTVFVSVANRDKRSLVFPVKRLADLGFRVLATE 1004
                                                ******************************************************************* PP

                                 TIGR01369  973 gtakvleeagikaevvlkvseea......ekilellkeeeielvinltskkkkaaekgykirreave 1033
                                                gta++l+ +gi +e v+k+ +e        ++++++k++++++vin++  ++  + +gy ir +av+
  lcl|NCBI__GCF_000015305.1:WP_011779880.1 1005 GTAEMLRRNGIPCEEVRKHFQEFseglpqMSAVDAIKAGHVDMVINTPYGNSGPRIDGYEIRSAAVS 1071
                                                *******************99988899776788****************9999************** PP

                                 TIGR01369 1034 ykvplvteletaealle 1050
                                                +++p+vt++++a+a+++
  lcl|NCBI__GCF_000015305.1:WP_011779880.1 1072 MNIPCVTTVQGASAAVQ 1088
                                                **********9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1052 nodes)
Target sequences:                          1  (1112 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: 0.08u 0.03s 00:00:00.11 Elapsed: 00:00:00.10
# Mc/sec: 11.42
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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