Alignments for a candidate for asnB in Sulfurimonas denitrificans DSM 1251

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Sulfurimonas denitrificans DSM 1251

Align Putative asparagine synthetase [glutamine-hydrolyzing] 2; EC 6.3.5.4 (uncharacterized)
to candidate WP_011371822.1 SUDEN_RS00940 asparagine synthase (glutamine-hydrolyzing)

Query= curated2:Q58456
         (515 letters)



>NCBI__GCF_000012965.1:WP_011371822.1
          Length = 583

 Score =  245 bits (626), Expect = 3e-69
 Identities = 155/412 (37%), Positives = 226/412 (54%), Gaps = 37/412 (8%)

Query: 1   MCGINGIIRFGKEVIKEEINKMNKAIKHRGPDDEGIFIYNFKNYSIGLGHVRLAILDLSE 60
           MCGI      G   I    N++  ++KHRG D +   I N     +   H RL+I+DL E
Sbjct: 1   MCGI-----IGSTEINFNHNEVLNSLKHRGEDYQNYIIQN----EMFFAHTRLSIIDLDE 51

Query: 61  KGHQPMGYNVDEDKIIYRDDELDRADIIIVYNGEIYNYLELKEKFNLETETGTDTEVILK 120
           + +QPM ++                +I +V+NGEIYNY EL ++F+LE  T +D+EV+++
Sbjct: 52  EANQPMIFD----------------EITLVFNGEIYNYKELIKEFSLECVTKSDSEVLIR 95

Query: 121 LYNKLGFDCVKEFNGMWAFCIFDKKKGLIFCSRDRLGVKPFYYYWDGNEFIFSSELKGIL 180
           LY K GFD +    GM+AFCI+DK+K L FC+RDR G KP YYY +  +F F+SE+K IL
Sbjct: 96  LYQKFGFDFLNSLEGMFAFCIYDKEKNLFFCARDRFGKKPLYYYCEKGKFYFASEIKAIL 155

Query: 181 AVKEINKKENINKDAVELYFALGFIPSPYSIYKNTFKLEARQNLIFDLDKREIRKYYYWE 240
             K +     +N++A+  Y AL       + Y    KL A   L+      +I+   Y+ 
Sbjct: 156 --KMLKTTPKLNEEALWQYLALQSPQGENTFYSGVKKLPASSYLLH--QNSDIKVSTYYS 211

Query: 241 LPDYK-PIYDKKKLIEEGKKLLYDAVKIRMRSDVPVGAFLSGGLDSSTVVGVMREFTDLS 299
           L D K   YD+K+++++ +KLL DAV+ R+  DV V   LSGGLDSS +  +  +     
Sbjct: 212 LADIKITHYDEKQILKDVEKLLNDAVQKRLVGDVEVATLLSGGLDSSFITALYAK-KSKH 270

Query: 300 KLHTFSIGFE--GKYDETPYIKIVVDYFKTQHHHYYFKERDFEELIDKYSWIYDEPFGDY 357
           K+HTFSIG++    Y E  + K   +Y  T HH Y   + ++ E I+K     DEP  D 
Sbjct: 271 KVHTFSIGYDEHKHYCELGFAKAASEYIGTIHHEYKISKDEYLEAIEKVLEHLDEPMADS 330

Query: 358 SGFPTYKVS-EMARKFVTVVLSGDGGDEVFGGYMTH---LNGYRMDFIRKLP 405
           +  PTY +S E+  +   V LSG+G DE F GY  +   LN Y +   +K P
Sbjct: 331 ACIPTYILSKEIHNQGFKVCLSGEGSDESFLGYDNYFKMLNYYHLKNPQKTP 382


Lambda     K      H
   0.322    0.144    0.434 

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: 915
Number of extensions: 64
Number of successful extensions: 9
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: 515
Length of database: 583
Length adjustment: 36
Effective length of query: 479
Effective length of database: 547
Effective search space:   262013
Effective search space used:   262013
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 (21.9 bits)
S2: 53 (25.0 bits)

Align candidate WP_011371822.1 SUDEN_RS00940 (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.508279.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.4e-143  464.8   0.7   2.7e-143  464.6   0.7    1.0  1  NCBI__GCF_000012965.1:WP_011371822.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000012965.1:WP_011371822.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  464.6   0.7  2.7e-143  2.7e-143       1     517 []       2     517 ..       2     517 .. 0.88

  Alignments for each domain:
  == domain 1  score: 464.6 bits;  conditional E-value: 2.7e-143
                             TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsnekevv 72 
                                           Cgi+g  + + +        +e+l+ l+hRG D +++ ++   ++  ++h RL+iidl e  +QP+  ++  +
  NCBI__GCF_000012965.1:WP_011371822.1   2 CGIIGSTEINFN-------HNEVLNSLKHRGEDYQNYIIQ---NEMFFAHTRLSIIDLDEEaNQPMIFDE-IT 63 
                                           777777666443.......3567889*********95444...89*************9998*****999.79 PP

                             TIGR01536  73 ivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlGi 145
                                           +vfnGEIYN++eL +e+     e  tksD+EV++++y+++g ++++ LeGmFAf ++d++k+ +f aRDr+G+
  NCBI__GCF_000012965.1:WP_011371822.1  64 LVFNGEIYNYKELIKEFS---LECVTKSDSEVLIRLYQKFGFDFLNSLEGMFAFCIYDKEKNLFFCARDRFGK 133
                                           ****************99...5699************************************************ PP

                             TIGR01536 146 kPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakal...dgeekl 215
                                           kPLYy++e+gk++faSEiKa+l++ +++++l++eal+++l+lq+ + e+t++ +vk+l+++++l   +++ k+
  NCBI__GCF_000012965.1:WP_011371822.1 134 KPLYYYCEKGKFYFASEIKAILKMLKTTPKLNEEALWQYLALQSPQGENTFYSGVKKLPASSYLlhqNSDIKV 206
                                           *******************************************99999***************9965555566 PP

                             TIGR01536 216 eeywevekee.vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeaksevktFsigf 287
                                           ++y+++++ + ++ +e++  +++++ll+dav+krlv+dv+v++llSGGlDSs+++a+ +k++k++v+tFsig+
  NCBI__GCF_000012965.1:WP_011371822.1 207 STYYSLADIKiTHYDEKQILKDVEKLLNDAVQKRLVGDVEVATLLSGGLDSSFITALYAKKSKHKVHTFSIGY 279
                                           66999999995566889999***************************************************** PP

                             TIGR01536 288 edskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasiplyllsklarekgvkVvLs 360
                                           +++k++ e  +a+++++++gt h+e+ is++e+l+++e+v+ +l+ep+a++a+ip+y+lsk+++++g+kV Ls
  NCBI__GCF_000012965.1:WP_011371822.1 280 DEHKHYCELGFAKAASEYIGTIHHEYKISKDEYLEAIEKVLEHLDEPMADSACIPTYILSKEIHNQGFKVCLS 352
                                           ************************************************************************* PP

                             TIGR01536 361 GeGaDElfgGYeyfreakaeealelpeaselaekkl........llqaklakeselkellkakleeelkekee 425
                                           GeG+DE f GY+ ++++ +  +l+ p+ + +  +k+          q+ ++++ e+  +++ +   ++k    
  NCBI__GCF_000012965.1:WP_011371822.1 353 GEGSDESFLGYDNYFKMLNYYHLKNPQKTPFDLTKEweynnrrlNNQQVYQSSGETFTYAQLQRLFSKKIAPI 425
                                           *****************99999997776664433332222222133333333333333333333333333333 PP

                             TIGR01536 426 lkkelkee.......seleellrldlelllsdllrak.DrvsmahslEvRvPflDkelvelalsippelklrd 490
                                                             + l++ d+  ++ ++l  k Dr+smahslE+R+PflD++lve+ l ++ ++k+ d
  NCBI__GCF_000012965.1:WP_011371822.1 426 -------LhpyvstyPPEQWLTYIDFSIWIAEVLMTKvDRMSMAHSLELRAPFLDHHLVEYLLGVESSIKIGD 491
                                           .......14455554888999**************************************************86 PP

                             TIGR01536 491 gkeKvlLreaaeellPeeileRkKeaf 517
                                            ++K +L+++a+++lP++i +R+K++f
  NCBI__GCF_000012965.1:WP_011371822.1 492 -TNKAILKKIARNYLPNSIIDRRKKGF 517
                                           .68*********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (583 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 19.04
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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