Alignments for a candidate for carB in Pedobacter sp. GW460-11-11-14-LB5

GapMind for Amino acid biosynthesis

Alignments for a candidate for carB in Pedobacter sp. GW460-11-11-14-LB5

Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate CA265_RS20080 CA265_RS20080 carbamoyl phosphate synthase large subunit

Query= BRENDA::P00968
         (1073 letters)



>FitnessBrowser__Pedo557:CA265_RS20080
          Length = 945

 Score =  923 bits (2386), Expect = 0.0
 Identities = 486/932 (52%), Positives = 648/932 (69%), Gaps = 25/932 (2%)

Query: 1   MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
           MPK T I+S+LI+G+GPIVIGQACEFDYSG+QA  +L+EEG  V ++NSNPATIMTD  +
Sbjct: 1   MPKDTSIRSVLIIGSGPIVIGQACEFDYSGSQAALSLKEEGITVSIINSNPATIMTDKVI 60

Query: 61  ADATYIEPIHWEVVRKIIEKE-------RPDAVLPTMGGQTALNCALELERQGVLEEFGV 113
            D  Y+ P+  + +  I+++        + DAVLPTMGGQTALN   E E +GV E++GV
Sbjct: 61  GDHVYLRPLTVDSIEVILQEHIDSADLPKIDAVLPTMGGQTALNLCKEAEERGVWEKYGV 120

Query: 114 TMIGATADAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFT 173
            ++G    AI+K E+R  F   M  IG+  A S IA++  E    A ++G+P +IRPS+T
Sbjct: 121 KVVGVDVAAIEKTENREAFRQLMVDIGVGVAESKIANSFLEGKEAAQEIGYPLVIRPSYT 180

Query: 174 MGGSGGGIAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCS 233
           +GGSGGG  + +EEF+    RGL+ SPT E+L++++++GWKEYE+E++RD NDN II+CS
Sbjct: 181 LGGSGGGFVHKKEEFDAALKRGLEASPTHEVLVEKAVLGWKEYELELLRDSNDNVIIICS 240

Query: 234 IENFDAMGIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNG 293
           IENFD MGIHTGDSITVAPA TL+D+ YQ MRN ++ ++R IG   GG NVQF+VNP + 
Sbjct: 241 IENFDPMGIHTGDSITVAPAMTLSDRCYQEMRNQAIKMMRAIGNFAGGCNVQFSVNPVDD 300

Query: 294 RLIVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSID 353
            +I IE+NPRVSRSSALASKATG+PIAK+AAKLA+GY LDE+ N IT   T A FEP++D
Sbjct: 301 EIIAIEINPRVSRSSALASKATGYPIAKIAAKLAIGYNLDEIENQIT-KTTSAYFEPTLD 359

Query: 354 YVVTKIPRFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKV 413
           YV+ K+PR+NF+KF GAN  L  QMKSVGEVMAIGRT  E+LQKA + LE+   G    +
Sbjct: 360 YVIVKVPRWNFDKFKGANKELGLQMKSVGEVMAIGRTFIEALQKACQSLEINRAG----L 415

Query: 414 SLDDPEA--LTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVR 471
             D  +   + +I   L+ A  +R++ I DA   G+ ++ +  +T ID+WFL QI+ELV 
Sbjct: 416 GADGRQVRNIEEIMDGLEHASWNRLFLIKDAMAMGVPLESIRKVTKIDKWFLNQIQELVL 475

Query: 472 LEEKVAEVGITGLNADFLRQLKRKGFADARLAKLAG-VREAEIRKLRDQYDLHPVYKRVD 530
           LE ++    +  +  DF   LK+KGF+D ++A L G V E E+   R    ++ VYK VD
Sbjct: 476 LETELKRYSLNNIPQDFFVTLKQKGFSDIQIAWLLGNVTEDEVYDRRKALGINRVYKMVD 535

Query: 531 TCAAEFATDTAYMYSTYEEECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALR 590
           TCAAEF   T Y YST+EEE E+ PS DR+K++VLG GPNRIGQGIEFDY CVH  LA +
Sbjct: 536 TCAAEFPAKTPYYYSTFEEENESVPS-DRKKVIVLGSGPNRIGQGIEFDYSCVHGLLAAK 594

Query: 591 EDGYETIMVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKL 650
           E G+E IM+NCNPETVSTD++ +D+LYFEPV  E V EI+ +EKP GVIVQ GGQT LK+
Sbjct: 595 ETGFEAIMINCNPETVSTDFNMADKLYFEPVFWEHVREIIELEKPVGVIVQLGGQTALKM 654

Query: 651 ARALEAAGVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGY 710
           A  L   G+ +IGTS + +D AEDR RF   ++ L +  P        E A+  A E+GY
Sbjct: 655 AEKLTEKGIKIIGTSFENMDIAEDRGRFSDLLKDLDIPYPKYGVAENAEEAIVVANEVGY 714

Query: 711 PLVVRPSYVLGGRAMEIVYDEADLRRYFQTAVSVSNDAP---VLLDHFLDDAVEVDVDAI 767
           P++VRPSYVLGG+ M IV ++ DL +     V +  D P   VL+DHFLD A E + D+I
Sbjct: 715 PVLVRPSYVLGGQGMSIVINDEDLEK---AVVKLLGDLPGNRVLIDHFLDRAEEAESDSI 771

Query: 768 CDGEMVLIGGIMEHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLMN 827
            DGE V I G+MEHIE AG+HSGDS   LP ++LS+ +   M +   K+A  L VRGL+N
Sbjct: 772 SDGEDVHIVGMMEHIEPAGIHSGDSFAVLPTFSLSETVTKAMEEYSIKIAKALDVRGLLN 831

Query: 828 VQFAVKNNEVYLIEVNPRAARTVPFVSKATGVPLAKVAARVMAG-KSLAEQGVTKEVIPP 886
           +QFA+K+ +VY+IE NPRA+RTVPF++KA  VP   +AA++M G   L +  + +++   
Sbjct: 832 IQFAIKDEKVYVIEANPRASRTVPFIAKAYDVPYINIAAKIMLGVAKLKDFTIVRKL--E 889

Query: 887 YYSVKEVVLPFNKFPGVDPLLGPEMRSTGEVM 918
            Y++KE V  + KFP V   LGPEM+STGE +
Sbjct: 890 GYAIKEPVFSYEKFPEVAKELGPEMKSTGEAI 921



 Score =  209 bits (531), Expect = 1e-57
 Identities = 137/400 (34%), Positives = 209/400 (52%), Gaps = 25/400 (6%)

Query: 557 TDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMVNCNPETVSTDYDTSDRL 616
           T    ++++G GP  IGQ  EFDY    A+L+L+E+G    ++N NP T+ TD    D +
Sbjct: 5   TSIRSVLIIGSGPIVIGQACEFDYSGSQAALSLKEEGITVSIINSNPATIMTDKVIGDHV 64

Query: 617 YFEPVTLEDVLEIVR-------IEKPKGVIVQYGGQTPLKLARALEAAGV------PVIG 663
           Y  P+T++ +  I++       + K   V+   GGQT L L +  E  GV       V+G
Sbjct: 65  YLRPLTVDSIEVILQEHIDSADLPKIDAVLPTMGGQTALNLCKEAEERGVWEKYGVKVVG 124

Query: 664 TSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYPLVVRPSYVLGGR 723
               AI++ E+RE F+  +  + +    +    +     E A+EIGYPLV+RPSY LGG 
Sbjct: 125 VDVAAIEKTENREAFRQLMVDIGVGVAESKIANSFLEGKEAAQEIGYPLVIRPSYTLGGS 184

Query: 724 AMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDG-EMVLIGGIMEHI 782
               V+ + +     +  +  S    VL++  +    E +++ + D  + V+I   +E+ 
Sbjct: 185 GGGFVHKKEEFDAALKRGLEASPTHEVLVEKAVLGWKEYELELLRDSNDNVIIICSIENF 244

Query: 783 EQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFEL-QVRGLMNVQFAVK--NNEVYL 839
           +  G+H+GDS    PA TLS      MR Q  K+   +    G  NVQF+V   ++E+  
Sbjct: 245 DPMGIHTGDSITVAPAMTLSDRCYQEMRNQAIKMMRAIGNFAGGCNVQFSVNPVDDEIIA 304

Query: 840 IEVNPRAARTVPFVSKATGVPLAKVAARVMAGKSL--AEQGVTK------EVIPPYYSVK 891
           IE+NPR +R+    SKATG P+AK+AA++  G +L   E  +TK      E    Y  VK
Sbjct: 305 IEINPRVSRSSALASKATGYPIAKIAAKLAIGYNLDEIENQITKTTSAYFEPTLDYVIVK 364

Query: 892 EVVLPFNKFPGVDPLLGPEMRSTGEVMGVGRTFAEAFAKA 931
                F+KF G +  LG +M+S GEVM +GRTF EA  KA
Sbjct: 365 VPRWNFDKFKGANKELGLQMKSVGEVMAIGRTFIEALQKA 404


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: 2545
Number of extensions: 126
Number of successful extensions: 20
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 1073
Length of database: 945
Length adjustment: 45
Effective length of query: 1028
Effective length of database: 900
Effective search space:   925200
Effective search space used:   925200
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: 57 (26.6 bits)

Align candidate CA265_RS20080 CA265_RS20080 (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.12058.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 1314.9   1.6          0 1314.7   1.6    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS20080  CA265_RS20080 carbamoyl phosphat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS20080  CA265_RS20080 carbamoyl phosphate synthase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1314.7   1.6         0         0       1     931 [.       2     937 ..       2     945 .] 0.97

  Alignments for each domain:
  == domain 1  score: 1314.7 bits;  conditional E-value: 0
                                  TIGR01369   1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePl 68 
                                                pk+++i++vl+iGsGpivigqA+EFDYsGsqa ++lkeegi+v ++nsn+At+mtd+ + d+vY+ Pl
  lcl|FitnessBrowser__Pedo557:CA265_RS20080   2 PKDTSIRSVLIIGSGPIVIGQACEFDYSGSQAALSLKEEGITVSIINSNPATIMTDKVIGDHVYLRPL 69 
                                                6889**************************************************************** PP

                                  TIGR01369  69 tveavekiiekE.......rpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRe 129
                                                tv ++e i+++        ++Da+l+t+GGqtaLnl  e ee+Gv ekygvk++G++v ai+k+e+Re
  lcl|FitnessBrowser__Pedo557:CA265_RS20080  70 TVDSIEVILQEHidsadlpKIDAVLPTMGGQTALNLCKEAEERGVWEKYGVKVVGVDVAAIEKTENRE 137
                                                ******998754444445589*********************************************** PP

                                  TIGR01369 130 kFkealkeineevakseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalka 197
                                                +F++++ +i++ va+s+i++s  e  eaa+eigyP+++R+++tlgG+G+g+++++ee+ +  +++l+a
  lcl|FitnessBrowser__Pedo557:CA265_RS20080 138 AFRQLMVDIGVGVAESKIANSFLEGKEAAQEIGYPLVIRPSYTLGGSGGGFVHKKEEFDAALKRGLEA 205
                                                ******************************************************************** PP

                                  TIGR01369 198 spikqvlvekslagwkEiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRd 265
                                                sp+++vlvek++ gwkE+E+E +RDs+dn+ii+c+iEn+Dp+G+HtGdsi+vaP+ tL+d+ yq +R+
  lcl|FitnessBrowser__Pedo557:CA265_RS20080 206 SPTHEVLVEKAVLGWKEYELELLRDSNDNVIIICSIENFDPMGIHTGDSITVAPAMTLSDRCYQEMRN 273
                                                ******************************************************************** PP

                                  TIGR01369 266 aslkiirelg.vegecnvqfaldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLde 332
                                                +++k++r++g  +g+cnvqf+++P + +++ iE+npRvsRssALAskAtGyPiAk+aakla+Gy+Lde
  lcl|FitnessBrowser__Pedo557:CA265_RS20080 274 QAIKMMRAIGnFAGGCNVQFSVNPVDDEIIAIEINPRVSRSSALASKATGYPIAKIAAKLAIGYNLDE 341
                                                *********836777***************************************************** PP

                                  TIGR01369 333 lkndvtketvAsfEPslDYvvvkiPrwdldkfekvdrklgtqmksvGEvmaigrtfeealqkalrsle 400
                                                ++n++tk+t+A fEP+lDYv+vk+Prw++dkf++++++lg qmksvGEvmaigrtf ealqka +sle
  lcl|FitnessBrowser__Pedo557:CA265_RS20080 342 IENQITKTTSAYFEPTLDYVIVKVPRWNFDKFKGANKELGLQMKSVGEVMAIGRTFIEALQKACQSLE 409
                                                ******************************************************************** PP

                                  TIGR01369 401 ekllglklkekeaesdeeleealkkpndrRlfaiaealrrgvsveevyeltkidrffleklkklvele 468
                                                ++  gl  + +++ + ee+++ l++++ +Rlf i +a+  gv +e++ ++tkid++fl+++++lv le
  lcl|FitnessBrowser__Pedo557:CA265_RS20080 410 INRAGLGADGRQVRNIEEIMDGLEHASWNRLFLIKDAMAMGVPLESIRKVTKIDKWFLNQIQELVLLE 477
                                                *********9********************************************************** PP

                                  TIGR01369 469 keleeeklkelkkellkkakklGfsdeqiaklvk.vseaevrklrkelgivpvvkrvDtvaaEfeakt 535
                                                +el++ +l++++++ + ++k++Gfsd qia l++ v+e+ev + rk+lgi  v+k+vDt+aaEf+akt
  lcl|FitnessBrowser__Pedo557:CA265_RS20080 478 TELKRYSLNNIPQDFFVTLKQKGFSDIQIAWLLGnVTEDEVYDRRKALGINRVYKMVDTCAAEFPAKT 545
                                                ******************************988538999***************************** PP

                                  TIGR01369 536 pYlYstyeeekddvevtekkkvlvlGsGpiRigqgvEFDycavhavlalreagyktilinynPEtvst 603
                                                pY+Yst+eee +++  +++kkv+vlGsGp+Rigqg+EFDy++vh++la +e+g+++i+in+nPEtvst
  lcl|FitnessBrowser__Pedo557:CA265_RS20080 546 PYYYSTFEEE-NESVPSDRKKVIVLGSGPNRIGQGIEFDYSCVHGLLAAKETGFEAIMINCNPETVST 612
                                                **********.888889999************************************************ PP

                                  TIGR01369 604 DydiadrLyFeeltvedvldiiekekvegvivqlgGqtalnlakeleeagvkilGtsaesidraEdRe 671
                                                D+++ad+LyFe++  e+v +iie ek+ gvivqlgGqtal++a++l+e+g+ki+Gts+e++d+aEdR 
  lcl|FitnessBrowser__Pedo557:CA265_RS20080 613 DFNMADKLYFEPVFWEHVREIIELEKPVGVIVQLGGQTALKMAEKLTEKGIKIIGTSFENMDIAEDRG 680
                                                ******************************************************************** PP

                                  TIGR01369 672 kFsklldelgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgGrameiveneeeleryleeavev 739
                                                +Fs ll++l+i+ pk+ +a++ eea  +a+e+gyPvlvRpsyvlgG++m+iv n+e+le+ + + +  
  lcl|FitnessBrowser__Pedo557:CA265_RS20080 681 RFSDLLKDLDIPYPKYGVAENAEEAIVVANEVGYPVLVRPSYVLGGQGMSIVINDEDLEKAVVKLLGD 748
                                                ******************************************************************** PP

                                  TIGR01369 740 skekPvlidkyledavEvdvDavadgeevliagileHiEeaGvHsGDstlvlppqklseevkkkikei 807
                                                 + + vlid++l+ a E++ D ++dge+v i+g++eHiE aG+HsGDs++vlp+ +lse v+k+++e+
  lcl|FitnessBrowser__Pedo557:CA265_RS20080 749 LPGNRVLIDHFLDRAEEAESDSISDGEDVHIVGMMEHIEPAGIHSGDSFAVLPTFSLSETVTKAMEEY 816
                                                ******************************************************************** PP

                                  TIGR01369 808 vkkiakelkvkGllniqfvvkdeevyviEvnvRasRtvPfvskalgvplvklavkvllgkkleelekg 875
                                                + kiak+l+v+Gllniqf++kde+vyviE+n+RasRtvPf++ka +vp++++a+k++lg    +    
  lcl|FitnessBrowser__Pedo557:CA265_RS20080 817 SIKIAKALDVRGLLNIQFAIKDEKVYVIEANPRASRTVPFIAKAYDVPYINIAAKIMLGVAKLKD--- 881
                                                **********************************************************9654442... PP

                                  TIGR01369 876 vkkekksklvavkaavfsfsklagvdvvlgpemkstGEvmgigrdleeallkalla 931
                                                 +   k + +a+k++vfs++k+ +v   lgpemkstGE++ + +dle+ +++ l +
  lcl|FitnessBrowser__Pedo557:CA265_RS20080 882 FTIVRKLEGYAIKEPVFSYEKFPEVAKELGPEMKSTGEAIRFIKDLEDPYFRKLYK 937
                                                345667789**************************************999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1052 nodes)
Target sequences:                          1  (945 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: 0.05u 0.03s 00:00:00.08 Elapsed: 00:00:00.07
# Mc/sec: 12.90
//
[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