Alignments for a candidate for asnB in Methanothermobacter thermautotrophicus Delta H

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Methanothermobacter thermautotrophicus Delta H

Align Putative asparagine synthetase [glutamine-hydrolyzing] 1; EC 6.3.5.4 (uncharacterized)
to candidate WP_010876053.1 MTH_RS01915 asparagine synthase (glutamine-hydrolyzing)

Query= curated2:Q58516
         (541 letters)



>NCBI__GCF_000008645.1:WP_010876053.1
          Length = 469

 Score =  278 bits (710), Expect = 4e-79
 Identities = 199/525 (37%), Positives = 289/525 (55%), Gaps = 91/525 (17%)

Query: 1   MCSISGIIVKDNQISAKYSIDMMKILKHRGRDNSGLLLDDEVIYFNDF-EDVEDLEEEMI 59
           MC+I+G    D  +  +   +M+ +L+HRG D +G+  D  ++      EDV++  +   
Sbjct: 4   MCAIAGFRGDDAPVKVQ---EMLDVLRHRGPDATGIYHDSRIVIRTATGEDVKEAPQS-- 58

Query: 60  GNLSLAHNRLAIVGRYGVQPIPNEDETIWLVCNGEIYNYIELREYLKQNHEFRTDSDNEV 119
             +++ HN L+IVG  G QP+  +     LV NGEIYN  EL           T SD+E+
Sbjct: 59  AEIAVGHNLLSIVG--GPQPVSGDGV---LVFNGEIYNQEELNW---------TGSDSEL 104

Query: 120 IIHLYE------EEKLE----ELDGDYAFAIYDKSKNVVRLARDMFGVKPLFYVDRDKYF 169
           I+ L E      E+ L     ++DGDYAFA  D      R  +D  GVKPL++       
Sbjct: 105 ILDLIEGHGGDLEDALRFTVNKIDGDYAFAYTDGENLASR--QDPVGVKPLYHSGE---- 158

Query: 170 AFASERKALWHLLINIDGCERDLDELNSKIKTLKPNSQLIYYLDDNRFEI-IEGFKKLEL 228
           AFASE+KALW + +               ++TL P   +I     N  ++ + G  + E 
Sbjct: 159 AFASEKKALWRIGLR-------------NVETLPPGHAMI-----NGVKVKLRGLPRAEP 200

Query: 229 NYMKERSYEEAKEYLDRALKNSVLKRVRGLDKVGIICSGGVDSSLIAKLASLYCEVILYA 288
           +   +   EE +E L  AL+ SV +RVRGLD+  ++ SGGVDS+L+A L   + +V LY 
Sbjct: 201 S---DAEPEELRENLKSALRESVERRVRGLDEAALVFSGGVDSTLLAVLLDEHIDVRLYT 257

Query: 289 VGTENSEDLIYAERLAKDLNLKLRKKIISEEEYEEYVFKVAKAIDEVDLMKIGVGIPIYV 348
           VG   S D  +A R A DL ++L    ++E+   E +  V  AI+E +LMKIGV +P+Y+
Sbjct: 258 VGLPGSSDPQFASRAAADLGMELEVLEVTEDTIREALPHVLGAIEEYNLMKIGVAMPLYL 317

Query: 349 ASEMANEDGLKVVLSGQGADELFGGYARHERIYRERGEEELKKELLKDVYNLYKVNLERD 408
           ASE A+ DG +V+ SGQGADELF GY R+ R+     E  L+  L  D+ N++ VNLERD
Sbjct: 318 ASEAASADGYRVMFSGQGADELFAGYHRYRRLL---AEGRLEDALRHDLENIHHVNLERD 374

Query: 409 DHCTMANGVELRVPFLDEEVVEIALSIPIEYKMSELSNRPYAESNISLKSEPINGLKNTN 468
           D  TMAN VELRVPFLD +++ +AL+IP + K                    I G ++  
Sbjct: 375 DAVTMANSVELRVPFLDLQLIGVALTIPADLK--------------------IRGPED-- 412

Query: 469 LNIKCVRSVRKKILRDVASQY-LPDYIAYRPKKAAQYGSGGEKMI 512
                   +RK+ILR+ A +  +P+YIA RPKKAAQYGSG +K++
Sbjct: 413 -------ELRKRILREAALEMGVPEYIAMRPKKAAQYGSGIDKVL 450


Lambda     K      H
   0.318    0.138    0.388 

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: 599
Number of extensions: 33
Number of successful extensions: 6
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: 541
Length of database: 469
Length adjustment: 34
Effective length of query: 507
Effective length of database: 435
Effective search space:   220545
Effective search space used:   220545
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: 52 (24.6 bits)

Align candidate WP_010876053.1 MTH_RS01915 (asparagine synthase (glutamine-hydrolyzing))
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.20326.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.6e-116  375.5   0.0    8.9e-90  288.0   0.0    2.7  2  lcl|NCBI__GCF_000008645.1:WP_010876053.1  MTH_RS01915 asparagine synthase 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000008645.1:WP_010876053.1  MTH_RS01915 asparagine synthase (glutamine-hydrolyzing)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  288.0   0.0   8.9e-90   8.9e-90       1     383 [.       5     355 ..       5     356 .. 0.94
   2 !   85.3   0.2   2.5e-28   2.5e-28     435     515 ..     354     439 ..     350     441 .. 0.93

  Alignments for each domain:
  == domain 1  score: 288.0 bits;  conditional E-value: 8.9e-90
                                 TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkd...............e.keenailghrRL 53 
                                               C+iag+  ++a       +++eml++l+hRGPDa+g+++d               + ++++ ++gh+ L
  lcl|NCBI__GCF_000008645.1:WP_010876053.1   5 CAIAGFRGDDAP-----VKVQEMLDVLRHRGPDATGIYHDsrivirtatgedvkeApQSAEIAVGHNLL 68 
                                               9******99875.....6789********************************9643455556666666 PP

                                 TIGR01536  54 aiidlsegaQPlsnekevvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeew......g.ee 115
                                               +i+      QP+s+++  v+vfnGEIYN+eeL+          +t sD+E+iL+++e +      + + 
  lcl|NCBI__GCF_000008645.1:WP_010876053.1  69 SIVGG---PQPVSGDG--VLVFNGEIYNQEELN----------WTGSDSELILDLIEGHggdledAlRF 122
                                               66654...8*******..***************..........9***************9999986699 PP

                                 TIGR01536 116 lverLeGmFAfalwdekkgelflaRDrlGikPLYyaseqgkllfaSEiKallalk..eikaeldkeala 182
                                               +v++++G++Afa++d   ++l++++D++G+kPLY++ e    +faSE+Kal+++   ++++ ++++a++
  lcl|NCBI__GCF_000008645.1:WP_010876053.1 123 TVNKIDGDYAFAYTDG--ENLASRQDPVGVKPLYHSGE----AFASEKKALWRIGlrNVETLPPGHAMI 185
                                               ****************..9*******************....9************99************ PP

                                 TIGR01536 183 elltlqlvptektlfkevkelepakaldgeekleeywevekeevkeseeelveelrelledavkkrlva 251
                                               ++++++         +++ ++ep++a+ +ee +e+                   l+++l+++v++r+++
  lcl|NCBI__GCF_000008645.1:WP_010876053.1 186 NGVKVK--------LRGLPRAEPSDAE-PEELREN-------------------LKSALRESVERRVRG 226
                                               ******........59**********8.8777775...................*************** PP

                                 TIGR01536 252 dvpvgvllSGGlDSslvaaiakkeaksevktFsigfedskdldeskaarkvadelgtehkevliseeev 320
                                                +++++++SGG+DS+l+a++++++++  v+++++g+++s+d +   +a+++a++lg+e++ ++++e+++
  lcl|NCBI__GCF_000008645.1:WP_010876053.1 227 LDEAALVFSGGVDSTLLAVLLDEHID--VRLYTVGLPGSSDPQ---FASRAAADLGMELEVLEVTEDTI 290
                                               ************************99..***************...*********************** PP

                                 TIGR01536 321 lkeleevilale..eptairasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeeal 383
                                                ++l++v+ a+e  ++++i  ++plyl+s++a+++g++V++sG+GaDElf+GY+++r+  ae +l
  lcl|NCBI__GCF_000008645.1:WP_010876053.1 291 REALPHVLGAIEeyNLMKIGVAMPLYLASEAASADGYRVMFSGQGADELFAGYHRYRRLLAEGRL 355
                                               ************9*********************************************9998776 PP

  == domain 2  score: 85.3 bits;  conditional E-value: 2.5e-28
                                 TIGR01536 435 eleellrldlelllsdllrakDrvsmahslEvRvPflDkelvelalsippelklr...dgkeKvlLrea 500
                                               +le++lr+dle++++ +l+++D v+ma+s+E+RvPflD +l+ +al+ip++lk+r   d+ +K++Lrea
  lcl|NCBI__GCF_000008645.1:WP_010876053.1 354 RLEDALRHDLENIHHVNLERDDAVTMANSVELRVPFLDLQLIGVALTIPADLKIRgpeDELRKRILREA 422
                                               68999**************************************************999999******** PP

                                 TIGR01536 501 aee.llPeeileR.kKe 515
                                               a e  +Pe+i++R kK+
  lcl|NCBI__GCF_000008645.1:WP_010876053.1 423 ALEmGVPEYIAMRpKKA 439
                                               99989********5555 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (469 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: 0.07u 0.01s 00:00:00.08 Elapsed: 00:00:00.07
# Mc/sec: 3.25
//
[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