Aligments for a candidate for carB in Magnetospirillum magneticum AMB-1

GapMind for Amino acid biosynthesis

Aligments for a candidate for carB in Magnetospirillum magneticum AMB-1

Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate WP_011383145.1 AMB_RS03605 carbamoyl-phosphate synthase large subunit

Query= BRENDA::P00968
         (1073 letters)



>NCBI__GCF_000009985.1:WP_011383145.1
          Length = 1085

 Score = 1293 bits (3347), Expect = 0.0
 Identities = 672/1071 (62%), Positives = 820/1071 (76%), Gaps = 20/1071 (1%)

Query: 1    MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
            MPKRTDIKSILI+GAGPIVIGQACEFDYSG QACKAL++EGYRVILVNSNPATIMTDP +
Sbjct: 1    MPKRTDIKSILIIGAGPIVIGQACEFDYSGVQACKALKDEGYRVILVNSNPATIMTDPGL 60

Query: 61   ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
            ADATYIEPI  E+V KIIEKERPDA+LPTMGGQTALN A++L   G+LE+FGV MI A  
Sbjct: 61   ADATYIEPITPEIVAKIIEKERPDALLPTMGGQTALNTAMKLADMGILEKFGVEMIAAKR 120

Query: 121  DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180
            D I KAEDR  F  AM KIGLE+ +S +  T++EA      VG P IIRPSFT+ G+GGG
Sbjct: 121  DVIAKAEDRLLFRDAMDKIGLESPKSRMVKTLQEAREALDFVGLPAIIRPSFTLAGTGGG 180

Query: 181  IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM 240
            IAYN  E+E I + GL  SP  E+L++ES++GWKEYEMEVVRDK DNCII+CSIEN D M
Sbjct: 181  IAYNVAEYEHIVSGGLAASPVHEVLVEESVLGWKEYEMEVVRDKKDNCIIICSIENVDPM 240

Query: 241  GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM 300
            G+HTGDSITVAPA TLTDKEYQIMRNAS+AVLREIGV+TGGSNVQFAVNPK+GR+ VIEM
Sbjct: 241  GVHTGDSITVAPALTLTDKEYQIMRNASLAVLREIGVDTGGSNVQFAVNPKDGRMTVIEM 300

Query: 301  NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP 360
            NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDEL NDIT G TPASFEP+IDYVVTKIP
Sbjct: 301  NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELTNDIT-GCTPASFEPTIDYVVTKIP 359

Query: 361  RFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFD----PKVSLD 416
            RF FEKF GA+  LTT MKSVGE MAIGRT QESLQK LR +E G TG D    P     
Sbjct: 360  RFTFEKFPGADPNLTTSMKSVGEAMAIGRTFQESLQKGLRSMETGLTGLDEVEIPGAGAG 419

Query: 417  DPEALTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKV 476
            D +    ++  L     DR+  IA AFR GL++D V      D+WFL Q++ +V  E ++
Sbjct: 420  DMK--DAVKSALAQPRHDRLLVIAQAFRFGLTIDEVHAACFYDKWFLAQLKGIVDAEAEI 477

Query: 477  AEVGITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEF 536
               G+  ++A  L +LK+ GF+D RLAKL+G    E    R+  ++ PV+KR+DTCAAEF
Sbjct: 478  RAKGLP-IDAPGLLRLKKMGFSDQRLAKLSGKSLVETAFRREVLNVKPVFKRIDTCAAEF 536

Query: 537  ATDTAYMYSTYE------EECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALR 590
             + TAYMYS YE       ECE++PS DR+K+++LGGGPNRIGQGIEFDYCCVHA+ AL 
Sbjct: 537  PSSTAYMYSCYEGDGVNPPECESDPS-DRDKVIILGGGPNRIGQGIEFDYCCVHAAYALD 595

Query: 591  EDGYETIMVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIE----KPKGVIVQYGGQT 646
            E G ETIMVNCNPETVSTDYDTSDRLYFEP+T E V+++VR E    K  G IVQ+GGQT
Sbjct: 596  EAGKETIMVNCNPETVSTDYDTSDRLYFEPLTAETVIDLVRKEQSNGKVLGCIVQFGGQT 655

Query: 647  PLKLARALEAAGVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAK 706
            PLKLA ALE AG+P++GTSPD+ID AEDRERFQ  + +L LKQPAN T  ++E A++ A+
Sbjct: 656  PLKLAHALEQAGIPILGTSPDSIDLAEDRERFQKMLHQLGLKQPANGTARSLEEAIKVAE 715

Query: 707  EIGYPLVVRPSYVLGGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDA 766
            +IGYP+V+RPS+VLGGRAM+IVYD   L RY   AV VS D PVL+D++L DA+EVDVDA
Sbjct: 716  KIGYPVVIRPSFVLGGRAMQIVYDHEALERYMVEAVKVSGDDPVLIDYYLKDAIEVDVDA 775

Query: 767  ICDGEMVLIGGIMEHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLM 826
            +CDG  V + GIM+HIE+AG+HSGDSACSLP Y+L +     + +Q   +A  L V GLM
Sbjct: 776  LCDGNQVYVAGIMQHIEEAGIHSGDSACSLPPYSLDKATIAELERQTAAMAKALNVVGLM 835

Query: 827  NVQFAVKNNEVYLIEVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVIPP 886
            N Q+A+K+ ++Y++EVNPRA+RTVPFV+KATGVP+AK+AARVMAG++LA  G++      
Sbjct: 836  NCQYAIKDGDIYILEVNPRASRTVPFVAKATGVPIAKIAARVMAGETLASFGLSTRPELK 895

Query: 887  YYSVKEVVLPFNKFPGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRAL 946
            + +VKE V PF +FPGVD LLGPEM+STGEVMG+   FA AFAK+QLG+ + +   G A 
Sbjct: 896  HVAVKEAVFPFARFPGVDILLGPEMKSTGEVMGIDSDFARAFAKSQLGAGTNLPTEGGAF 955

Query: 947  LSVREGDKERVVDLAAKLLKQGFELDATHGTAIVLGEAGI-NPRLVNKVHEGRPHIQDRI 1005
            +SVR+GDK  +V++A +LL+ GF++ AT GTA  L + G+    +VNKV EGRPH  D +
Sbjct: 956  ISVRDGDKPAMVEIARRLLEMGFKVMATDGTAFYLKDRGVTGVTIVNKVLEGRPHCVDAM 1015

Query: 1006 KNGEYTYIINTTSGRRAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNA 1056
             NG+   ++NTT G +A++DS  IRR+AL   + + TT+ G  A   A+ A
Sbjct: 1016 MNGQVQLVVNTTEGSQAVKDSFSIRRTALTNNIPHYTTVAGARAAVEAIEA 1066


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: 3035
Number of extensions: 123
Number of successful extensions: 18
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: 1085
Length adjustment: 46
Effective length of query: 1027
Effective length of database: 1039
Effective search space:  1067053
Effective search space used:  1067053
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_011383145.1 AMB_RS03605 (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.11611.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 1506.3   0.0          0 1506.1   0.0    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011383145.1  AMB_RS03605 carbamoyl-phosphate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011383145.1  AMB_RS03605 carbamoyl-phosphate synthase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1506.1   0.0         0         0       1    1051 [.       2    1063 ..       2    1064 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1506.1 bits;  conditional E-value: 0
                                 TIGR01369    1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYieP 67  
                                                pkr+dik++l+iG+GpivigqA+EFDYsG qa+kalk+eg++v+Lvnsn+At+mtd+ lad++YieP
  lcl|NCBI__GCF_000009985.1:WP_011383145.1    2 PKRTDIKSILIIGAGPIVIGQACEFDYSGVQACKALKDEGYRVILVNSNPATIMTDPGLADATYIEP 68  
                                                689**************************************************************** PP

                                 TIGR01369   68 ltveavekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkea 134 
                                                +t+e+v+kiiekErpDa+l+t+GGqtaLn a++l ++G+Lek+gv+++ +k ++i+kaedR +F++a
  lcl|NCBI__GCF_000009985.1:WP_011383145.1   69 ITPEIVAKIIEKERPDALLPTMGGQTALNTAMKLADMGILEKFGVEMIAAKRDVIAKAEDRLLFRDA 135 
                                                ******************************************************************* PP

                                 TIGR01369  135 lkeineevakseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspik 201 
                                                +++i++e +ks++v++ +ea ea + +g+P i+R++ftl+GtG+gia+n +e +++v+ +l+asp++
  lcl|NCBI__GCF_000009985.1:WP_011383145.1  136 MDKIGLESPKSRMVKTLQEAREALDFVGLPAIIRPSFTLAGTGGGIAYNVAEYEHIVSGGLAASPVH 202 
                                                ******************************************************************* PP

                                 TIGR01369  202 qvlvekslagwkEiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdasl 268 
                                                +vlve+s+ gwkE+E+EvvRD+kdncii+c+iEn+Dp+GvHtGdsi+vaP+ tLtdkeyq++R+asl
  lcl|NCBI__GCF_000009985.1:WP_011383145.1  203 EVLVEESVLGWKEYEMEVVRDKKDNCIIICSIENVDPMGVHTGDSITVAPALTLTDKEYQIMRNASL 269 
                                                ******************************************************************* PP

                                 TIGR01369  269 kiirelgvege.cnvqfaldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelk 334 
                                                +++re+gv+++ +nvqfa++P++ r++viE+npRvsRssALAskAtG+PiAkvaaklavGy+Ldel+
  lcl|NCBI__GCF_000009985.1:WP_011383145.1  270 AVLREIGVDTGgSNVQFAVNPKDGRMTVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELT 336 
                                                ********9988******************************************************* PP

                                 TIGR01369  335 ndvtketvAsfEPslDYvvvkiPrwdldkfekvdrklgtqmksvGEvmaigrtfeealqkalrslee 401 
                                                nd+t+ t+AsfEP++DYvv+kiPr+ ++kf ++d +l+t+mksvGE maigrtf+e+lqk+lrs+e+
  lcl|NCBI__GCF_000009985.1:WP_011383145.1  337 NDITGCTPASFEPTIDYVVTKIPRFTFEKFPGADPNLTTSMKSVGEAMAIGRTFQESLQKGLRSMET 403 
                                                ******************************************************************* PP

                                 TIGR01369  402 kllg...lklkek.eaesdeeleealkkpndrRlfaiaealrrgvsveevyeltkidrffleklkkl 464 
                                                +l+g   ++++ + +  +++++++al +p ++Rl++ia+a+r g++++ev+ ++ +d++fl +lk +
  lcl|NCBI__GCF_000009985.1:WP_011383145.1  404 GLTGldeVEIPGAgAGDMKDAVKSALAQPRHDRLLVIAQAFRFGLTIDEVHAACFYDKWFLAQLKGI 470 
                                                ****4443444441445667788999***************************************** PP

                                 TIGR01369  465 velekeleeeklkelkkellkkakklGfsdeqiaklvkvseaevrklrkelgivpvvkrvDtvaaEf 531 
                                                v++e e++ + l  +++  l ++kk+Gfsd+++akl ++s  e    r+ l++ pv+kr+Dt+aaEf
  lcl|NCBI__GCF_000009985.1:WP_011383145.1  471 VDAEAEIRAKGLP-IDAPGLLRLKKMGFSDQRLAKLSGKSLVETAFRREVLNVKPVFKRIDTCAAEF 536 
                                                *******966655.9**************************************************** PP

                                 TIGR01369  532 eaktpYlYstyeee.....kddvevtekkkvlvlGsGpiRigqgvEFDycavhavlalreagyktil 593 
                                                +++t+Y+Ys ye++     + +++ ++++kv++lG+Gp+Rigqg+EFDyc+vha+ al eag++ti+
  lcl|NCBI__GCF_000009985.1:WP_011383145.1  537 PSSTAYMYSCYEGDgvnppECESDPSDRDKVIILGGGPNRIGQGIEFDYCCVHAAYALDEAGKETIM 603 
                                                ************99777766677788889************************************** PP

                                 TIGR01369  594 inynPEtvstDydiadrLyFeeltvedvldiiekekve....gvivqlgGqtalnlakeleeagvki 656 
                                                +n+nPEtvstDyd++drLyFe+lt e+v+d+++ke+ +    g+ivq+gGqt+l+la++le+ag++i
  lcl|NCBI__GCF_000009985.1:WP_011383145.1  604 VNCNPETVSTDYDTSDRLYFEPLTAETVIDLVRKEQSNgkvlGCIVQFGGQTPLKLAHALEQAGIPI 670 
                                                ***********************************866223379*********************** PP

                                 TIGR01369  657 lGtsaesidraEdRekFsklldelgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgGrameiv 723 
                                                lGts++sid aEdRe+F+k+l++lg+kqp++ +a+s+eea ++a++igyPv++Rps+vlgGram+iv
  lcl|NCBI__GCF_000009985.1:WP_011383145.1  671 LGTSPDSIDLAEDRERFQKMLHQLGLKQPANGTARSLEEAIKVAEKIGYPVVIRPSFVLGGRAMQIV 737 
                                                ******************************************************************* PP

                                 TIGR01369  724 eneeeleryleeavevskekPvlidkyledavEvdvDavadgeevliagileHiEeaGvHsGDstlv 790 
                                                +++e lery+ eav+vs + Pvlid yl+da+EvdvDa++dg++v++agi++HiEeaG+HsGDs+++
  lcl|NCBI__GCF_000009985.1:WP_011383145.1  738 YDHEALERYMVEAVKVSGDDPVLIDYYLKDAIEVDVDALCDGNQVYVAGIMQHIEEAGIHSGDSACS 804 
                                                ******************************************************************* PP

                                 TIGR01369  791 lppqklseevkkkikeivkkiakelkvkGllniqfvvkdeevyviEvnvRasRtvPfvskalgvplv 857 
                                                lpp +l++ +  +++++++++ak+l+v+Gl+n q+++kd+++y++Evn+RasRtvPfv+ka+gvp++
  lcl|NCBI__GCF_000009985.1:WP_011383145.1  805 LPPYSLDKATIAELERQTAAMAKALNVVGLMNCQYAIKDGDIYILEVNPRASRTVPFVAKATGVPIA 871 
                                                ******************************************************************* PP

                                 TIGR01369  858 klavkvllgkkleelekgvkkekksklvavkaavfsfsklagvdvvlgpemkstGEvmgigrdleea 924 
                                                k+a++v++g++l++   g++++++ k+vavk+avf+f+++ gvd++lgpemkstGEvmgi++d+++a
  lcl|NCBI__GCF_000009985.1:WP_011383145.1  872 KIAARVMAGETLAS--FGLSTRPELKHVAVKEAVFPFARFPGVDILLGPEMKSTGEVMGIDSDFARA 936 
                                                **************..56799********************************************** PP

                                 TIGR01369  925 llkallaskakikkkgsvllsvkdkdkeellelakklaekglkvyategtakvleeagik.aevvlk 990 
                                                ++k++l ++++++++g +++sv+d dk +++e+a++l e+g+kv+at+gta +l+++g++ ++ v+k
  lcl|NCBI__GCF_000009985.1:WP_011383145.1  937 FAKSQLGAGTNLPTEGGAFISVRDGDKPAMVEIARRLLEMGFKVMATDGTAFYLKDRGVTgVTIVNK 1003
                                                *********************************************************9973678899 PP

                                 TIGR01369  991 vseeaekilellkeeeielvinltskkkkaaekgykirreaveykvplvteletaeallea 1051
                                                v e ++++++++++++++lv+n+t+ +++a++++++irr+a+++++p+ t++++a+a++ea
  lcl|NCBI__GCF_000009985.1:WP_011383145.1 1004 VLEGRPHCVDAMMNGQVQLVVNTTE-GSQAVKDSFSIRRTALTNNIPHYTTVAGARAAVEA 1063
                                                9*********************997.8889999***********************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1052 nodes)
Target sequences:                          1  (1085 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: 0.07u 0.03s 00:00:00.10 Elapsed: 00:00:00.09
# Mc/sec: 11.81
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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