Alignments for a candidate for carB in Shewanella amazonensis SB2B

GapMind for Amino acid biosynthesis

Alignments for a candidate for carB in Shewanella amazonensis SB2B

Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate 6938384 Sama_2503 carbamoyl phosphate synthase large subunit (RefSeq)

Query= BRENDA::P00968
         (1073 letters)



>FitnessBrowser__SB2B:6938384
          Length = 1076

 Score = 1802 bits (4667), Expect = 0.0
 Identities = 900/1073 (83%), Positives = 980/1073 (91%), Gaps = 1/1073 (0%)

Query: 1    MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
            MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM
Sbjct: 1    MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60

Query: 61   ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
            ADATYIEPIHWEVVR II KERPDA+LPTMGGQTALNCALELE +GVL+EF V MIGATA
Sbjct: 61   ADATYIEPIHWEVVRNIIAKERPDAILPTMGGQTALNCALELEAKGVLKEFNVEMIGATA 120

Query: 121  DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180
            DAIDKAEDR RFD AMKKIGLE  R+GIAH+MEEA AV   VGFPCIIRPSFTMGGSGGG
Sbjct: 121  DAIDKAEDRARFDKAMKKIGLECPRAGIAHSMEEAYAVLDQVGFPCIIRPSFTMGGSGGG 180

Query: 181  IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM 240
            IAYN+EEFEEIC++GL+LSPT ELLIDESLIGWKEYEMEVVRD+NDNCIIVCSIENFDAM
Sbjct: 181  IAYNKEEFEEICSQGLELSPTNELLIDESLIGWKEYEMEVVRDRNDNCIIVCSIENFDAM 240

Query: 241  GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM 300
            G+HTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQF ++P  GR++VIEM
Sbjct: 241  GVHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFGISPTTGRMVVIEM 300

Query: 301  NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP 360
            NPRVSRSSALASKATGFPIAKVAAKLAVG+TLDELMNDITGGRTPASFEPSIDYVVTK+P
Sbjct: 301  NPRVSRSSALASKATGFPIAKVAAKLAVGFTLDELMNDITGGRTPASFEPSIDYVVTKVP 360

Query: 361  RFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKVSLDDPEA 420
            RFNFEKFAGANDRLTTQMKSVGEVMAIGRT QES+QKALRGLEV   GFDP V L D +A
Sbjct: 361  RFNFEKFAGANDRLTTQMKSVGEVMAIGRTFQESVQKALRGLEVSRNGFDPIVDLSDADA 420

Query: 421  LTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEVG 480
            L KIR ELK+ GADRIWYI DAFRAGLSV+ +F LTNIDRWFLVQIEE+++LE KV E+G
Sbjct: 421  LQKIRHELKEPGADRIWYIGDAFRAGLSVEDIFALTNIDRWFLVQIEEIIQLEAKVKELG 480

Query: 481  ITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATDT 540
            +TG++ DFLR+LKRKGF+DAR++ L G+ E EIRKLR+++++ PVYKRVDTCAAEFATDT
Sbjct: 481  VTGIDEDFLRKLKRKGFSDARMSALLGISEGEIRKLRERFNVFPVYKRVDTCAAEFATDT 540

Query: 541  AYMYSTYEEECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMVN 600
            AYMYSTYEEECEANPS D++KIMVLGGGPNRIGQGIEFDYCCVHA+LALREDGYETIMVN
Sbjct: 541  AYMYSTYEEECEANPS-DKDKIMVLGGGPNRIGQGIEFDYCCVHAALALREDGYETIMVN 599

Query: 601  CNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAAGVP 660
            CNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIV YGGQTPLKLARALEAAGVP
Sbjct: 600  CNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVHYGGQTPLKLARALEAAGVP 659

Query: 661  VIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYPLVVRPSYVL 720
            +IGTSPDAIDRAEDRERFQ A++RL +KQP N TVT +E AV  A+ IGYPLVVRPSYVL
Sbjct: 660  IIGTSPDAIDRAEDRERFQQAIKRLNMKQPENDTVTTVEGAVIAAERIGYPLVVRPSYVL 719

Query: 721  GGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDGEMVLIGGIME 780
            GGRAMEIVYDE DLRRYF  AVSVSN +PVLLD FLDDA EVD+DA+CDGE V+IG IME
Sbjct: 720  GGRAMEIVYDEQDLRRYFNEAVSVSNASPVLLDRFLDDATEVDIDAVCDGETVVIGAIME 779

Query: 781  HIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLMNVQFAVKNNEVYLI 840
            HIEQAGVHSGDSACSLP YTLS+ IQD MR+QV KLAFEL V GLMNVQFAVK+NE+Y+I
Sbjct: 780  HIEQAGVHSGDSACSLPPYTLSKAIQDQMREQVSKLAFELGVVGLMNVQFAVKDNEIYMI 839

Query: 841  EVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVIPPYYSVKEVVLPFNKF 900
            EVNPRAARTVPFVSKATGVPLAK+AARVMAG+SL +Q  TKEVIPP+YSVKEVVLPFNKF
Sbjct: 840  EVNPRAARTVPFVSKATGVPLAKIAARVMAGQSLKQQNFTKEVIPPFYSVKEVVLPFNKF 899

Query: 901  PGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALLSVREGDKERVVDL 960
            PGVDPLLGPEMRSTGEVMGVG TFAEA+AK++LGS   + + GRALLSVR  DK +V DL
Sbjct: 900  PGVDPLLGPEMRSTGEVMGVGDTFAEAYAKSELGSIKDVPRSGRALLSVRNSDKNKVADL 959

Query: 961  AAKLLKQGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIKNGEYTYIINTTSGR 1020
            AAKLL+ G+ELDATHGTA++LGEAGINPRLVNKVHEGRPHI DRIKNGEY YI+NTT GR
Sbjct: 960  AAKLLELGYELDATHGTAVILGEAGINPRLVNKVHEGRPHILDRIKNGEYAYIVNTTEGR 1019

Query: 1021 RAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNADATEKVISVQEMHAQIK 1073
            +AIEDSR +RR+AL+YKV+Y TTLN  FA  MA NAD   KV SVQE+H ++K
Sbjct: 1020 QAIEDSRQLRRAALRYKVNYTTTLNAAFANCMAHNADDRNKVASVQELHERVK 1072


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: 3369
Number of extensions: 130
Number of successful extensions: 12
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: 1076
Length adjustment: 45
Effective length of query: 1028
Effective length of database: 1031
Effective search space:  1059868
Effective search space used:  1059868
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 6938384 Sama_2503 (carbamoyl phosphate synthase large subunit (RefSeq))
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.19006.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 1584.8   0.0          0 1584.6   0.0    1.0  1  lcl|FitnessBrowser__SB2B:6938384  Sama_2503 carbamoyl phosphate sy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6938384  Sama_2503 carbamoyl phosphate synthase large subunit (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1584.6   0.0         0         0       1    1050 [.       2    1051 ..       2    1053 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1584.6 bits;  conditional E-value: 0
                         TIGR01369    1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePltveavek 75  
                                        pkr+dik++l++G+GpivigqA+EFDYsG+qa+kal+eeg++v+Lvnsn+At+mtd+e+ad++YieP+++e+v++
  lcl|FitnessBrowser__SB2B:6938384    2 PKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEMADATYIEPIHWEVVRN 76  
                                        689************************************************************************ PP

                         TIGR01369   76 iiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealkeineevakseives 150 
                                        ii kErpDail+t+GGqtaLn+a+ele kGvL++++v+++G++ +ai+kaedR +F++a+k+i++e +++ i++s
  lcl|FitnessBrowser__SB2B:6938384   77 IIAKERPDAILPTMGGQTALNCALELEAKGVLKEFNVEMIGATADAIDKAEDRARFDKAMKKIGLECPRAGIAHS 151 
                                        *************************************************************************** PP

                         TIGR01369  151 veealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikqvlvekslagwkEiEyEvvRDskd 225 
                                        +eea ++ +++g+P+i+R++ft+gG+G+gia+n+ee++e+++++l++sp++++l+++sl gwkE+E+EvvRD++d
  lcl|FitnessBrowser__SB2B:6938384  152 MEEAYAVLDQVGFPCIIRPSFTMGGSGGGIAYNKEEFEEICSQGLELSPTNELLIDESLIGWKEYEMEVVRDRND 226 
                                        *************************************************************************** PP

                         TIGR01369  226 nciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslkiirelgvege.cnvqfaldPeskryvviEvn 299 
                                        nciivc+iEn+D++GvHtGdsi+vaP+qtLtdkeyq++R+as++++re+gve++ +nvqf+++P++ r+vviE+n
  lcl|FitnessBrowser__SB2B:6938384  227 NCIIVCSIENFDAMGVHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGgSNVQFGISPTTGRMVVIEMN 301 
                                        ****************************************************988******************** PP

                         TIGR01369  300 pRvsRssALAskAtGyPiAkvaaklavGysLdelkndvtk.etvAsfEPslDYvvvkiPrwdldkfekvdrklgt 373 
                                        pRvsRssALAskAtG+PiAkvaaklavG++Ldel+nd+t+ +t+AsfEPs+DYvv+k+Pr++++kf++++++l+t
  lcl|FitnessBrowser__SB2B:6938384  302 PRVSRSSALASKATGFPIAKVAAKLAVGFTLDELMNDITGgRTPASFEPSIDYVVTKVPRFNFEKFAGANDRLTT 376 
                                        ***************************************879********************************* PP

                         TIGR01369  374 qmksvGEvmaigrtfeealqkalrsleekllglk..lkekeaesdeeleealkkpndrRlfaiaealrrgvsvee 446 
                                        qmksvGEvmaigrtf+e++qkalr le +  g++  ++ + a + ++++++lk+p ++R+++i +a+r+g+sve+
  lcl|FitnessBrowser__SB2B:6938384  377 QMKSVGEVMAIGRTFQESVQKALRGLEVSRNGFDpiVDLSDADALQKIRHELKEPGADRIWYIGDAFRAGLSVED 451 
                                        ********************************762233445666788899************************* PP

                         TIGR01369  447 vyeltkidrffleklkklvelekeleeeklkelkkellkkakklGfsdeqiaklvkvseaevrklrkelgivpvv 521 
                                        ++ lt+idr+fl +++++++le +++e  ++ ++++ l+k+k++Gfsd+++++l++ se e+rklr++ ++ pv+
  lcl|FitnessBrowser__SB2B:6938384  452 IFALTNIDRWFLVQIEEIIQLEAKVKELGVTGIDEDFLRKLKRKGFSDARMSALLGISEGEIRKLRERFNVFPVY 526 
                                        *************************************************************************** PP

                         TIGR01369  522 krvDtvaaEfeaktpYlYstyeeekddvevtekkkvlvlGsGpiRigqgvEFDycavhavlalreagyktiliny 596 
                                        krvDt+aaEf ++t+Y+Ystyeee++ ++ ++k+k++vlG+Gp+Rigqg+EFDyc+vha+lalre gy+ti++n+
  lcl|FitnessBrowser__SB2B:6938384  527 KRVDTCAAEFATDTAYMYSTYEEECEANP-SDKDKIMVLGGGPNRIGQGIEFDYCCVHAALALREDGYETIMVNC 600 
                                        ************************66655.5556***************************************** PP

                         TIGR01369  597 nPEtvstDydiadrLyFeeltvedvldiiekekvegvivqlgGqtalnlakeleeagvkilGtsaesidraEdRe 671 
                                        nPEtvstDyd++drLyFe++t+edvl+i++ ek++gviv++gGqt+l+la++le+agv+i+Gts+++idraEdRe
  lcl|FitnessBrowser__SB2B:6938384  601 NPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVHYGGQTPLKLARALEAAGVPIIGTSPDAIDRAEDRE 675 
                                        *************************************************************************** PP

                         TIGR01369  672 kFsklldelgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgGrameiveneeeleryleeavevskekPvl 746 
                                        +F++++++l++kqp++ ++t+ve a+ +a++igyP++vRpsyvlgGrameiv++e++l+ry++eav+vs+ +Pvl
  lcl|FitnessBrowser__SB2B:6938384  676 RFQQAIKRLNMKQPENDTVTTVEGAVIAAERIGYPLVVRPSYVLGGRAMEIVYDEQDLRRYFNEAVSVSNASPVL 750 
                                        *************************************************************************** PP

                         TIGR01369  747 idkyledavEvdvDavadgeevliagileHiEeaGvHsGDstlvlppqklseevkkkikeivkkiakelkvkGll 821 
                                        +d++l+da+Evd+Dav+dge+v+i +i+eHiE+aGvHsGDs+++lpp +ls+ ++++++e+v+k+a el v+Gl+
  lcl|FitnessBrowser__SB2B:6938384  751 LDRFLDDATEVDIDAVCDGETVVIGAIMEHIEQAGVHSGDSACSLPPYTLSKAIQDQMREQVSKLAFELGVVGLM 825 
                                        *************************************************************************** PP

                         TIGR01369  822 niqfvvkdeevyviEvnvRasRtvPfvskalgvplvklavkvllgkkleelekgvkkekksklvavkaavfsfsk 896 
                                        n+qf+vkd+e+y+iEvn+Ra+RtvPfvska+gvpl+k+a++v++g++l++++   +ke  + +++vk++v++f+k
  lcl|FitnessBrowser__SB2B:6938384  826 NVQFAVKDNEIYMIEVNPRAARTVPFVSKATGVPLAKIAARVMAGQSLKQQN--FTKEVIPPFYSVKEVVLPFNK 898 
                                        **************************************************55..69******************* PP

                         TIGR01369  897 lagvdvvlgpemkstGEvmgigrdleeallkallaskakikkkgsvllsvkdkdkeellelakklaekglkvyat 971 
                                        + gvd++lgpem+stGEvmg+g++++ea++k+ l s + +++ g++llsv+++dk+++ +la+kl e+g+++ at
  lcl|FitnessBrowser__SB2B:6938384  899 FPGVDPLLGPEMRSTGEVMGVGDTFAEAYAKSELGSIKDVPRSGRALLSVRNSDKNKVADLAAKLLELGYELDAT 973 
                                        *************************************************************************** PP

                         TIGR01369  972 egtakvleeagikaevvlkvseeaekilellkeeeielvinltskkkkaaekgykirreaveykvplvteletae 1046
                                        +gta +l eagi+ ++v+kv+e +++il+ +k++e+ +++n+t+ +++a e++ ++rr+a++ykv++ t+l++a 
  lcl|FitnessBrowser__SB2B:6938384  974 HGTAVILGEAGINPRLVNKVHEGRPHILDRIKNGEYAYIVNTTE-GRQAIEDSRQLRRAALRYKVNYTTTLNAAF 1047
                                        *****************************************997.88899999*****************99987 PP

                         TIGR01369 1047 alle 1050
                                        a ++
  lcl|FitnessBrowser__SB2B:6938384 1048 ANCM 1051
                                        7665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1052 nodes)
Target sequences:                          1  (1076 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: 13.30
//
[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