Alignments for a candidate for asnB in Hydrogenovibrio marinus DSM 11271

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.24629.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: 8.40
//
[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:

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