Alignments for a candidate for carB in Bacteroides thetaiotaomicron VPI-5482

GapMind for Amino acid biosynthesis

Alignments for a candidate for carB in Bacteroides thetaiotaomicron VPI-5482

Align Carbamoyl-phosphate synthase arginine-specific large chain; Arginine-specific carbamoyl-phosphate synthetase, ammonia chain; EC 6.3.5.5 (characterized)
to candidate 350085 BT0557 carbamyl phosphate synthetase (NCBI ptt file)

Query= SwissProt::P03965
         (1118 letters)



>FitnessBrowser__Btheta:350085
          Length = 1075

 Score = 1102 bits (2850), Expect = 0.0
 Identities = 574/1097 (52%), Positives = 760/1097 (69%), Gaps = 35/1097 (3%)

Query: 26   EGVNSVLVIGSGGLSIGQAGEFDYSGSQAIKALKEDNKFTILVNPNIATNQTSHSLADKI 85
            E +  VL++GSG L IG+AGEFDYSGSQA+KALKE+   TIL+NPNIAT QTS  +AD+I
Sbjct: 3    ENIKKVLLLGSGALKIGEAGEFDYSGSQALKALKEEGIETILINPNIATVQTSEGVADQI 62

Query: 86   YYLPVTPEYITYIIELERPDAILLTFGGQTGLNCGVALDESGVLAKYNVKVLGTPIKTLI 145
            Y+LPVTP ++  +I+ E+P+ I+L FGGQT LNCGVAL + G+L KYNVKVLGTP++ ++
Sbjct: 63   YFLPVTPYFVEKVIQKEKPEGIMLAFGGQTALNCGVALYKEGILEKYNVKVLGTPVQAIM 122

Query: 146  TSEDRDLFASALKDINIPIAESFACETVDEALEAAERVKYPVIVRSAYALGGLGSGFANN 205
             +EDR+LF   L +IN+   +S A E  ++A  AA+ + YPVIVR+AYALGGLGSGF +N
Sbjct: 123  DTEDRELFVQKLNEINVKTIKSEAVENAEDARRAAKELGYPVIVRAAYALGGLGSGFCDN 182

Query: 206  ASEMKELAAQSLSLAPQILVEKSLKGWKEVEYEVVRDRVGNCITVCNMENFDPLGVHTGD 265
              ++  L  ++ S +PQ+LVEKSL+GWKEVEYEVVRDR  NCITVCNMENFDPLG+HTG+
Sbjct: 183  EEQLDVLVEKAFSFSPQVLVEKSLRGWKEVEYEVVRDRFDNCITVCNMENFDPLGIHTGE 242

Query: 266  SMVFAPSQTLSDEEFHMLRSAAIKIIRHLGVIGECNVQYALQPDGLDYRVIEVNARLSRS 325
            S+V APSQTL++ E+H LR  AI+IIRH+G++GECNVQYA  P+  DYRVIEVNARLSRS
Sbjct: 243  SIVIAPSQTLTNSEYHKLRELAIRIIRHIGIVGECNVQYAFDPESEDYRVIEVNARLSRS 302

Query: 326  SALASKATGYPLAYTAAKIGLGYTLPELPNPITKTTVANFEPSLDYIVAKIPKWDLSKFQ 385
            SALASKATGYPLA+ AAK+GLGY L +L N +TKTT A FEP+LDY+V KIP+WDL KF 
Sbjct: 303  SALASKATGYPLAFVAAKLGLGYGLFDLKNSVTKTTSAFFEPALDYVVCKIPRWDLGKFH 362

Query: 386  YVDRSIGSSMKSVGEVMAIGRNYEEAFQKALRQVDPSLLGFQGSTEFG-DQLDEALRTPT 444
             VD+ +GSSMKSVGEVMAIGR +EEA QK LR +   + GF  + E     +D+ALR PT
Sbjct: 363  GVDKELGSSMKSVGEVMAIGRTFEEAIQKGLRMIGQGMHGFVENKELVIPDIDKALREPT 422

Query: 445  DRRVLAIGQALIHENYTVERVNELSKIDKWFLYKCMNIVNIYKEL----ESVKSLSDLSK 500
            D+R+  I +A     YT+++V+EL+KIDKWFL K MNI+   +E+     + K ++DL  
Sbjct: 423  DKRIFVISKA-FRAGYTIDQVHELTKIDKWFLQKLMNIMKTSEEMHEWGNNHKQIADLPV 481

Query: 501  DLLQRAKKLGFSDKQIAVTINKHASTNINELEIRSLRKTLGIIPFVKRIDTLAAEFPAQT 560
            +LL++AK  GFSD QIA  I          L +R  RK  GI+P VK+IDTLAAE+PAQT
Sbjct: 482  ELLRKAKVQGFSDFQIARAIGYEGDMENGSLYVRKYRKAAGILPVVKQIDTLAAEYPAQT 541

Query: 561  NYLYTTYNATKNDVEF--NENGMLVLGSGVYRIGSSVEFDWCAVNTAKTLRDQGKKTIMI 618
            NYLY TY+   NDV +  +   ++VLGSG YRIGSSVEFDWC V    T+R +G +++MI
Sbjct: 542  NYLYLTYSGVANDVHYLGDHKSIVVLGSGAYRIGSSVEFDWCGVQALNTIRKEGWRSVMI 601

Query: 619  NYNPETVSTDFDEVDRLYFEELSYERVMDIYELEQSEGCIISVGGQLPQNIALKLYDNGC 678
            NYNPETVSTD+D  DRLYF+EL++ERVMDI ELE   G I+S GGQ+P N+AL+L     
Sbjct: 602  NYNPETVSTDYDMCDRLYFDELTFERVMDILELENPHGVIVSTGGQIPNNLALRLDAQNI 661

Query: 679  NIMGTNPNDIDRAENRHKFSSILDSIDVDQPEWSELTSVEEAKLFASKVNYPVLIRPSYV 738
            +I+GT+   ID AE+R KFS++LD I VDQP W ELTS+E+   F  +V +PVL+RPSYV
Sbjct: 662  HILGTSAQSIDNAEDREKFSAMLDRIGVDQPRWRELTSLEDINEFVDEVGFPVLVRPSYV 721

Query: 739  LSGAAMSVVNNEEELKAKLTLASDVSPDHPVVMSKFIEGAQEIDVDAVAYNGNVLVHAIS 798
            LSGAAM+V +N+EEL+  L LA++VS  HPVV+S+FIE A+E+++DAVA NG ++ +AIS
Sbjct: 722  LSGAAMNVCSNQEELERFLKLAANVSKKHPVVVSQFIEHAKEVEMDAVAQNGEIIAYAIS 781

Query: 799  EHVENAGVHSGDASLVLPPQHLSDDVKIALKDIADKVAKAWKITGPFNMQIIKDGEHTLK 858
            EH+E AGVHSGDA++  PPQ L  +    +K I+ ++AKA  I+GPFN+Q +   ++ +K
Sbjct: 782  EHIEFAGVHSGDATIQFPPQKLYVETVRRIKRISREIAKALNISGPFNIQYLAK-DNDIK 840

Query: 859  VIECNIRASRSFPFVSKVLGVNFIEIAVKAFLGGDIVPKPVDLMLNKKYDYVATKVPQFS 918
            VIECN+RASRSFPFVSKVL +NFIE+A K  LG  +     +L    + DYV  K  QFS
Sbjct: 841  VIECNLRASRSFPFVSKVLKINFIELATKVMLGLPVEKPEKNLF---ELDYVGIKASQFS 897

Query: 919  FTRLAGADPFLGVEMASTGEVASFGRDLIESYWTAIQSTMNFHVPLPPSGILFGGDTSRE 978
            F RL  ADP LGV+MASTGEV   G D   +    +++ ++    +P   IL    T ++
Sbjct: 898  FNRLQKADPVLGVDMASTGEVGCIGSD---TSCAVLKAMLSVGYRIPKKNILLSTGTMKQ 954

Query: 979  Y--LGQVASIVATIGYRIYTTNETTKTYLQEHIKEKNAKVSLIKFPKNDKR-KLRELFQE 1035
               +   A ++   GY+++ T  T KT+ +  I+      +L+ +P  +   +  E+   
Sbjct: 955  KADMMDAARMLVNKGYKLFATGGTHKTFAENGIES-----TLVYWPSEEGHPQALEMLHN 1009

Query: 1036 YDIKAVFNLASKRAESTDDVDYIMRRNAIDFAIPLFNEPQTALLFAKCLKAKIAEKIKIL 1095
             +I  V N+         D  Y +RR AID  +PL    + A  F         + I I 
Sbjct: 1010 KEIDMVVNIPKNLTAGELDNGYKIRRAAIDLNVPLITNARLASAFINAFCTMTVDDIAI- 1068

Query: 1096 ESHDVIVPPEVRSWDEF 1112
                       +SW+E+
Sbjct: 1069 -----------KSWEEY 1074


Lambda     K      H
   0.317    0.134    0.380 

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: 2754
Number of extensions: 115
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: 1118
Length of database: 1075
Length adjustment: 46
Effective length of query: 1072
Effective length of database: 1029
Effective search space:  1103088
Effective search space used:  1103088
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 (21.6 bits)
S2: 58 (26.9 bits)

Align candidate 350085 BT0557 (carbamyl phosphate synthetase (NCBI ptt file))
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.11614.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 1577.2   0.4          0 1577.0   0.4    1.0  1  lcl|FitnessBrowser__Btheta:350085  BT0557 carbamyl phosphate synthe


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:350085  BT0557 carbamyl phosphate synthetase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1577.0   0.4         0         0       3    1051 ..       2    1057 ..       1    1058 [. 0.98

  Alignments for each domain:
  == domain 1  score: 1577.0 bits;  conditional E-value: 0
                          TIGR01369    3 redikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePltveaveki 76  
                                         +e+ikkvl++GsG+++ig+A+EFDYsGsqalkalkeegie++L+n+niAtv+t+e +ad++Y++P+t+++vek+
  lcl|FitnessBrowser__Btheta:350085    2 KENIKKVLLLGSGALKIGEAGEFDYSGSQALKALKEEGIETILINPNIATVQTSEGVADQIYFLPVTPYFVEKV 75  
                                         789*********************************************************************** PP

                          TIGR01369   77 iekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealkeineevakseives 150 
                                         i+kE+p++i+l++GGqtaLn++v l ++G+Leky+vk+lGt+v+ai+++edRe+F ++l+ein++++kse+ve+
  lcl|FitnessBrowser__Btheta:350085   76 IQKEKPEGIMLAFGGQTALNCGVALYKEGILEKYNVKVLGTPVQAIMDTEDRELFVQKLNEINVKTIKSEAVEN 149 
                                         ************************************************************************** PP

                          TIGR01369  151 veealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikqvlvekslagwkEiEyEvvRDsk 224 
                                          e+a +aa+e+gyPvivRaa++lgG Gsg+++nee+l  lveka++ s  +qvlveksl gwkE+EyEvvRD++
  lcl|FitnessBrowser__Btheta:350085  150 AEDARRAAKELGYPVIVRAAYALGGLGSGFCDNEEQLDVLVEKAFSFS--PQVLVEKSLRGWKEVEYEVVRDRF 221 
                                         ************************************************..9*********************** PP

                          TIGR01369  225 dnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslkiirelgvegecnvqfaldPeskryvviEv 298 
                                         dnci+vcn+En+DplG+HtG+siv+aPsqtLt++ey++lR+ +++iir++g++gecnvq+a dPes++y+viEv
  lcl|FitnessBrowser__Btheta:350085  222 DNCITVCNMENFDPLGIHTGESIVIAPSQTLTNSEYHKLRELAIRIIRHIGIVGECNVQYAFDPESEDYRVIEV 295 
                                         ************************************************************************** PP

                          TIGR01369  299 npRvsRssALAskAtGyPiAkvaaklavGysLdelkndvtketvAsfEPslDYvvvkiPrwdldkfekvdrklg 372 
                                         n+R+sRssALAskAtGyP+A vaakl++Gy+L++lkn+vtk+t+A+fEP+lDYvv+kiPrwdl kf++vd++lg
  lcl|FitnessBrowser__Btheta:350085  296 NARLSRSSALASKATGYPLAFVAAKLGLGYGLFDLKNSVTKTTSAFFEPALDYVVCKIPRWDLGKFHGVDKELG 369 
                                         ************************************************************************** PP

                          TIGR01369  373 tqmksvGEvmaigrtfeealqkalrsleekllglklkekeaesdeeleealkkpndrRlfaiaealrrgvsvee 446 
                                         ++mksvGEvmaigrtfeea+qk+lr++ ++++g+ ++++ +++d +  +al++p+d+R+f+i +a+r+g+++++
  lcl|FitnessBrowser__Btheta:350085  370 SSMKSVGEVMAIGRTFEEAIQKGLRMIGQGMHGFVENKELVIPDID--KALREPTDKRIFVISKAFRAGYTIDQ 441 
                                         ************************************9999999988..9************************* PP

                          TIGR01369  447 vyeltkidrffleklkklvelekeleee.....klkelkkellkkakklGfsdeqiaklvkvseae......vr 509 
                                         v+eltkid++fl+kl++++++++e++e      ++ +l+ ell+kak +Gfsd qia++++ + +       vr
  lcl|FitnessBrowser__Btheta:350085  442 VHELTKIDKWFLQKLMNIMKTSEEMHEWgnnhkQIADLPVELLRKAKVQGFSDFQIARAIGYEGDMengslyVR 515 
                                         *************************9764433355599**********************965444456667** PP

                          TIGR01369  510 klrkelgivpvvkrvDtvaaEfeaktpYlYstyeeekddvevtek.kkvlvlGsGpiRigqgvEFDycavhavl 582 
                                         k+rk++gi+pvvk++Dt+aaE++a+t+YlY+ty++  +dv++  + k+++vlGsG++Rig++vEFD+c+v+a++
  lcl|FitnessBrowser__Btheta:350085  516 KYRKAAGILPVVKQIDTLAAEYPAQTNYLYLTYSGVANDVHYLGDhKSIVVLGSGAYRIGSSVEFDWCGVQALN 589 
                                         ***************************************998765599************************** PP

                          TIGR01369  583 alreagyktilinynPEtvstDydiadrLyFeeltvedvldiiekekvegvivqlgGqtalnlakeleeagvki 656 
                                         ++r++g ++++inynPEtvstDyd++drLyF+elt+e+v+di+e e+++gviv++gGq+++nla +l++++++i
  lcl|FitnessBrowser__Btheta:350085  590 TIRKEGWRSVMINYNPETVSTDYDMCDRLYFDELTFERVMDILELENPHGVIVSTGGQIPNNLALRLDAQNIHI 663 
                                         ************************************************************************** PP

                          TIGR01369  657 lGtsaesidraEdRekFsklldelgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgGrameiveneeele 730 
                                         lGtsa+sid+aEdRekFs++ld++g++qp+++e+ts+e+++e+++e+g+PvlvRpsyvl+G+am++++n+eele
  lcl|FitnessBrowser__Btheta:350085  664 LGTSAQSIDNAEDREKFSAMLDRIGVDQPRWRELTSLEDINEFVDEVGFPVLVRPSYVLSGAAMNVCSNQEELE 737 
                                         ************************************************************************** PP

                          TIGR01369  731 ryleeavevskekPvlidkyledavEvdvDavadgeevliagileHiEeaGvHsGDstlvlppqklseevkkki 804 
                                         r+l+ a++vsk++Pv++++++e+a+Ev++Dava+++e+++++i+eHiE aGvHsGD+t+++ppqkl  e++++i
  lcl|FitnessBrowser__Btheta:350085  738 RFLKLAANVSKKHPVVVSQFIEHAKEVEMDAVAQNGEIIAYAISEHIEFAGVHSGDATIQFPPQKLYVETVRRI 811 
                                         ************************************************************************** PP

                          TIGR01369  805 keivkkiakelkvkGllniqfvvkdeevyviEvnvRasRtvPfvskalgvplvklavkvllgkkleelekgvkk 878 
                                         k+i+++iak+l+++G++niq+++kd++++viE+n+RasR++Pfvsk+l++++++la+kv+lg  +e+ ek   +
  lcl|FitnessBrowser__Btheta:350085  812 KRISREIAKALNISGPFNIQYLAKDNDIKVIECNLRASRSFPFVSKVLKINFIELATKVMLGLPVEKPEK---N 882 
                                         *******************************************************************665...8 PP

                          TIGR01369  879 ekksklvavkaavfsfsklagvdvvlgpemkstGEvmgigrdleeallkallaskakikkkgsvllsvkdkdke 952 
                                           + ++v++ka++fsf++l+++d+vlg++m+stGEv +ig+d++ a+lka+l+++++i+kk+ +l++++ k+k 
  lcl|FitnessBrowser__Btheta:350085  883 LFELDYVGIKASQFSFNRLQKADPVLGVDMASTGEVGCIGSDTSCAVLKAMLSVGYRIPKKNILLSTGTMKQKA 956 
                                         8999********************************************************************** PP

                          TIGR01369  953 ellelakklaekglkvyategtakvleeagikaevvlkvseea.ekilellkeeeielvinltskkkk.aaekg 1024
                                         +++++a++l++kg+k++at gt+k+++e+gi++++v++ see  +++le+l+++ei++v+n++++ ++ + ++g
  lcl|FitnessBrowser__Btheta:350085  957 DMMDAARMLVNKGYKLFATGGTHKTFAENGIESTLVYWPSEEGhPQALEMLHNKEIDMVVNIPKNLTAgELDNG 1030
                                         **************************************99876699****************9986655899** PP

                          TIGR01369 1025 ykirreaveykvplvteletaeallea 1051
                                         ykirr+a++ +vpl+t++++a+a+++a
  lcl|FitnessBrowser__Btheta:350085 1031 YKIRRAAIDLNVPLITNARLASAFINA 1057
                                         ************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1052 nodes)
Target sequences:                          1  (1075 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: 0.06u 0.02s 00:00:00.08 Elapsed: 00:00:00.08
# Mc/sec: 13.29
//
[ok]

This GapMind analysis is from Apr 09 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