GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asnB in Hydrogenovibrio marinus DSM 11271

Align asparagine synthase (glutamine-hydrolysing) 3; EC 6.3.5.4 (characterized)
to candidate WP_029908049.1 P166_RS0101425 N-acetylglutaminylglutamine amidotransferase

Query= CharProtDB::CH_007942
         (614 letters)



>NCBI__GCF_000711315.1:WP_029908049.1
          Length = 601

 Score =  261 bits (666), Expect = 8e-74
 Identities = 192/630 (30%), Positives = 306/630 (48%), Gaps = 62/630 (9%)

Query: 1   MCGITGWVDFKKQLVQEKQTMDRMTDTLSKRGPDDSNVWGEHHVLFGHKRLAVVDI-EGG 59
           MCGI G + +  + V E  ++  M   L +RGPDD   W ++ V  GH+RL+++D+ + G
Sbjct: 1   MCGICGEIYWNGRGVSEA-SLTPMLKALERRGPDDGGTWIQNQVGLGHRRLSIIDLSDAG 59

Query: 60  RQPMACTYKGDTYTIIYNGELYNTEDLRKELRARGHQFERTSDTEVLLHSYIEWQEDCVD 119
            QPM      +  ++++NG +YN + LR  L   GH+F   SDTEV+L +Y +W  DCV 
Sbjct: 60  HQPMI----DNELSLVFNGCIYNYQSLRSLLIELGHEFCSHSDTEVILKAYRQWGMDCVT 115

Query: 120 HLNGIFAFAVWDEKRNLLFAARDRLGVKPFFYTKEGSSFLFGSEIKAILAHPDIKARVDR 179
              G+FAFAVWD+    L  ARDR G+KP +Y        F S  +A+LA  DI   +D 
Sbjct: 116 RFEGMFAFAVWDDHHQQLLIARDRFGIKPLYYAPVDGGVKFASNTQALLASGDINTEIDP 175

Query: 180 TGLSEIFGL-GPSRTPGTGIFKGIKEIRPAHALTFSKDGLNIWR-YWNVESEKHTD---- 233
            GL   F L G    P T I KGI+++ P H +  + DG    + YW++ +E+       
Sbjct: 176 IGLHHQFTLHGVIPAPYT-ILKGIRKLEPGHWMIVNPDGQMFKKSYWHLMAERPAGAENL 234

Query: 234 SFDDTVANVRSLFQDAVTRQL-VSDVPVCTFLSGGLDSSAITAIAAGHFEKEGKAPLHTY 292
           + +D +  +    + AV ++L  +DVPV   LSGGLDSS I A+ A    + G   + T+
Sbjct: 235 NEEDWINRIHDSLKQAVHKRLTAADVPVGVLLSGGLDSSLIVALLA----EAGVENIRTF 290

Query: 293 SIDYEENDKYFQASAFQPNDDGPWIEKMTEAFGTTHHKCVISQKDLVDHLEEAVLVKDLP 352
           SI +E+  +  + S F+ +D      ++ E + T H K +IS ++++  L  AV     P
Sbjct: 291 SIGFEDVPEE-KGSEFEYSD------QVVERYQTIHKKYLISNEEVLPRLPGAVDAMAEP 343

Query: 353 GMADVDSSLLWFCREIKKDFVVSLSGECADEIFGGYPWF--------------HTADVES 398
                  +      ++ KD  V +SG+ ADE+F GY W+                 +  +
Sbjct: 344 MFGQDAVAFYLLSEQVSKDVKVVMSGQGADEVFAGYFWYPQMAEAYEKLSPGEPPVNAFA 403

Query: 399 GFPWMRSTEERIKLLSDSWQKKLNLKEYVNAKYEETLAETPLLDGETGVDKARRQLFYLN 458
            F + R+ EE +++++  +       E+ N +  E  A T  LD    +D +        
Sbjct: 404 PFYFDRTHEEWLEMVNPKYHVHDVTSEWANDRLSEPGA-TTFLDQVLRLDAS-------- 454

Query: 459 MLWFMTNLLDRKDRMSMGASLEVRVPFADHRLVEYVWNIPWEMKMHDNREKGILRKALEG 518
               + + + R D M+M  SLE RVPF DH LVE   + P  +K  D   K +L+K   G
Sbjct: 455 -TLIVDDPVKRVDNMTMAWSLEARVPFLDHDLVELTMSAPESLKRKD--FKYVLKKIARG 511

Query: 519 ILPDDILYRKKSPYPKTHHPEYTKGVSEWLKTIRSQKDSVLHTLLDRKQLDQLL---ETE 575
           I+PD ++ R K  +P            +W+K + +   +    + +   ++ LL   E E
Sbjct: 512 IVPDSVIDRPKGYFPMPALKYVRDDFYQWMKDVLTSDAAKTRGIFNPDYIENLLANPENE 571

Query: 576 GSSFKVPWFGQLMKGPQLIAHLAQIHTWFE 605
            S   +       KG +L  H A +  W +
Sbjct: 572 ASFTAI-------KGSKL-WHAALLELWLQ 593


Lambda     K      H
   0.320    0.137    0.425 

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: 969
Number of extensions: 50
Number of successful extensions: 7
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: 614
Length of database: 601
Length adjustment: 37
Effective length of query: 577
Effective length of database: 564
Effective search space:   325428
Effective search space used:   325428
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)

Align candidate WP_029908049.1 P166_RS0101425 (N-acetylglutaminylglutamine amidotransferase)
to HMM TIGR01536 (asnB: asparagine synthase (glutamine-hydrolyzing) (EC 6.3.5.4))

# 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/TIGR01536.hmm
# target sequence database:        /tmp/gapView.19872.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01536  [M=517]
Accession:   TIGR01536
Description: asn_synth_AEB: asparagine synthase (glutamine-hydrolyzing)
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-138  449.0   0.0   1.7e-138  448.7   0.0    1.0  1  lcl|NCBI__GCF_000711315.1:WP_029908049.1  P166_RS0101425 N-acetylglutaminy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000711315.1:WP_029908049.1  P166_RS0101425 N-acetylglutaminylglutamine amidotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  448.7   0.0  1.7e-138  1.7e-138       1     516 [.       2     524 ..       2     525 .. 0.86

  Alignments for each domain:
  == domain 1  score: 448.7 bits;  conditional E-value: 1.7e-138
                                 TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsne 68 
                                               Cgi g +  +   ++ e+ +  ml++l++RGPD+ g+w++   ++++lghrRL+iidls++ +QP+ ++
  lcl|NCBI__GCF_000711315.1:WP_029908049.1   2 CGICGEIYWNGRGVS-EASLTPMLKALERRGPDDGGTWIQ---NQVGLGHRRLSIIDLSDAgHQPMIDN 66 
                                               999998877776555.589*********************...79**************999******9 PP

                                 TIGR01536  69 kevvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelf 137
                                               +   +vfnG IYN+++Lr  l+e G+eF ++sDtEViL+ay++wg ++v r+eGmFAfa+wd+++++l+
  lcl|NCBI__GCF_000711315.1:WP_029908049.1  67 E-LSLVFNGCIYNYQSLRSLLIELGHEFCSHSDTEVILKAYRQWGMDCVTRFEGMFAFAVWDDHHQQLL 134
                                               9.78***************************************************************** PP

                                 TIGR01536 138 laRDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlq.lvptektlfkevkelep 205
                                               +aRDr+GikPLYya  +g + faS  +alla  +i++e+d  +l++++tl+ + p + t+ k++++lep
  lcl|NCBI__GCF_000711315.1:WP_029908049.1 135 IARDRFGIKPLYYAPVDGGVKFASNTQALLASGDINTEIDPIGLHHQFTLHgVIPAPYTILKGIRKLEP 203
                                               **************************************************9999*************** PP

                                 TIGR01536 206 akal....dgeekleeywevekee....vkeseeelveelrelledavkkrlv.advpvgvllSGGlDS 265
                                               ++ +    dg+  +++yw++  e+     + +ee+ ++++ + l++av+krl  advpvgvllSGGlDS
  lcl|NCBI__GCF_000711315.1:WP_029908049.1 204 GHWMivnpDGQMFKKSYWHLMAERpagaENLNEEDWINRIHDSLKQAVHKRLTaADVPVGVLLSGGLDS 272
                                               ***9996555555566***999888887788899******************989************** PP

                                 TIGR01536 266 slvaaiakkeaksevktFsigfe..dskdldeskaarkvadelgtehkevliseeevlkeleevilale 332
                                               sl++a++++   ++++tFsigfe   +++ +e ++  +v++   t hk++lis+eevl  l+  + a+ 
  lcl|NCBI__GCF_000711315.1:WP_029908049.1 273 SLIVALLAEAGVENIRTFSIGFEdvPEEKGSEFEYSDQVVERYQTIHKKYLISNEEVLPRLPGAVDAMA 341
                                               ******9999999**********333444455669********************************** PP

                                 TIGR01536 333 eptairasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeealelpease.laekkl.... 396
                                               ep+  ++++  ylls++++++ vkVv+sG+GaDE+f+GY ++ ++  + + +l+  +  +++  +    
  lcl|NCBI__GCF_000711315.1:WP_029908049.1 342 EPMFGQDAVAFYLLSEQVSKD-VKVVMSGQGADEVFAGYFWYPQMAEA-YEKLSPGEPpVNA--Fapfy 406
                                               ********************9.********************996333.3332222222222..22333 PP

                                 TIGR01536 397 ..llqaklakeselkellkakleeelke.keelkkelkeeseleellrldlelllsdl.lrakDrvsma 461
                                                 ++++++ + ++ k  ++    + ++e  ++  +e  +++ l+++lrld+ +l+ d+ +++ D ++ma
  lcl|NCBI__GCF_000711315.1:WP_029908049.1 407 fdRTHEEWLEMVNPKYHVH----DVTSEwANDRLSEPGATTFLDQVLRLDASTLIVDDpVKRVDNMTMA 471
                                               3333333433333333333....22222022233333344889*******9988776626666****** PP

                                 TIGR01536 462 hslEvRvPflDkelvelalsippelklrdgkeKvlLreaaeellPeeileRkKea 516
                                               +slE+RvPflD++lvel +s p +lk   ++ K++L+++a++++P+++ +R+K  
  lcl|NCBI__GCF_000711315.1:WP_029908049.1 472 WSLEARVPFLDHDLVELTMSAPESLKR--KDFKYVLKKIARGIVPDSVIDRPKGY 524
                                               ***********************9875..678********************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (601 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 8.68
//
[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:

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:

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:

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:

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