Alignments for a candidate for asnB in Arcobacter nitrofigilis DSM 7299

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Arcobacter nitrofigilis DSM 7299

Align asparagine synthase (glutamine-hydrolysing) (EC 6.3.5.4) (characterized)
to candidate WP_013133950.1 ARNIT_RS00680 asparagine synthase (glutamine-hydrolyzing)

Query= BRENDA::B3KYI2
         (570 letters)



>NCBI__GCF_000092245.1:WP_013133950.1
          Length = 593

 Score =  149 bits (377), Expect = 2e-40
 Identities = 113/374 (30%), Positives = 186/374 (49%), Gaps = 53/374 (14%)

Query: 28  LRHRGPDWSGLHCHDDCFLAHQRLAIVD-PTSGDQPLYNEDKTVIVTVNGEIYNHKQLRQ 86
           + +RGPD+S +  H +    H RL+I+D     +QP+  +D  +++  NGEIYN+K+L  
Sbjct: 21  MNNRGPDYSKVFAHKNYQFGHTRLSIIDVDDEANQPMIFDD--ILIVFNGEIYNYKELI- 77

Query: 87  KLSSHKFRTGSDCEVIAHLYEEYGEEFVNMLDGMFAFVLLDTRDKSFIAARDAIGITPLY 146
           K  +    T SD EVI  LY++YG +F+N L+GMF+FV+ D + + +  ARD  G  P +
Sbjct: 78  KSENLLCSTSSDTEVIIRLYQKYGIDFLNKLNGMFSFVIFDLKQEKYFCARDRYGKKPFF 137

Query: 147 LGWGHDGSTWFASEMK---------------ALSDDCERFMSFPPGHIY----------- 180
             +  D    F+S +K               ALS   + F+S      Y           
Sbjct: 138 Y-YFKDNKFIFSSSIKSIIKILGFTPKLNKVALSQYLQYFVSLNDMTFYNDINKLEASSY 196

Query: 181 ---SSKQGGLRRWYNPHWFSE--DIPSTPYDPILLRETFERAVVKRMMTDVPFGVLLSGG 235
              SS +  ++++Y  + + +  D      D   + E   ++V  R++ DV  G LLSGG
Sbjct: 197 MLLSSNELFIKKYYKINTYKKVVDEKQALND---IEELLFKSVESRLVGDVEVGSLLSGG 253

Query: 236 LDSSLVASVVNRYLKESEAARQWGSQLHTFCIGLK---GSPDLKAAKEVADYLGTRHHEL 292
           +DSS ++S+              G +++TF +G        +L  A  V+  + + HH L
Sbjct: 254 IDSSFISSLYTNIT---------GKRINTFSVGYSDHISYSELDYASLVSKDINSIHHPL 304

Query: 293 YFTVQEGIDALEEVIYHIETYDVTTIRASTPMFLMSRKIKALGVKMVLSGEGSDEIFGGY 352
             +  + ID  +EVI  +E     +  A+ P++ +++ I   G+K+VLSGEGSDE+F GY
Sbjct: 305 EVSRNDFIDVFDEVIDALEEPHADS--AAFPLYCLTKLINKKGIKVVLSGEGSDELFLGY 362

Query: 353 LYFHKAPNKKEFHE 366
             + K     +F E
Sbjct: 363 DNYSKFLKYYKFKE 376



 Score = 34.3 bits (77), Expect = 1e-05
 Identities = 20/73 (27%), Positives = 37/73 (50%), Gaps = 9/73 (12%)

Query: 382 RANKSTAAWGVEARVPFLDKEFIDVAMSIDPEWKMIRRDLGRIEKWVLRNAFDDEKNPYL 441
           + ++ + A  +E R PFLD   +D   S+D + K      G   K++L+       + Y+
Sbjct: 464 KVDRISMANSIEVRTPFLDFRLVDYLFSVDTKLK-----TGDTNKYLLKKI----ASKYI 514

Query: 442 PKHILYRQKEQFS 454
           P+ I+ R K+ F+
Sbjct: 515 PEKIINRTKKGFN 527


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: 703
Number of extensions: 31
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 570
Length of database: 593
Length adjustment: 36
Effective length of query: 534
Effective length of database: 557
Effective search space:   297438
Effective search space used:   297438
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_013133950.1 ARNIT_RS00680 (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.31152.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-133  432.8   0.5   1.4e-133  432.6   0.5    1.0  1  lcl|NCBI__GCF_000092245.1:WP_013133950.1  ARNIT_RS00680 asparagine synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000092245.1:WP_013133950.1  ARNIT_RS00680 asparagine synthase (glutamine-hydrolyzing)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  432.6   0.5  1.4e-133  1.4e-133      23     517 .]      17     526 ..       2     526 .. 0.88

  Alignments for each domain:
  == domain 1  score: 432.6 bits;  conditional E-value: 1.4e-133
                                 TIGR01536  23 mletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsnekevvivfnGEIYNheeLreele 90 
                                                l +++ RGPD + v+ +   +n  +gh RL+iid+ +  +QP+  ++  +ivfnGEIYN++eL +  +
  lcl|NCBI__GCF_000092245.1:WP_013133950.1  17 ALSLMNNRGPDYSKVFAH---KNYQFGHTRLSIIDVDDEaNQPMIFDD-ILIVFNGEIYNYKELIKSEN 81 
                                               4568899***********...7**************9998*******9.79*************98777 PP

                                 TIGR01536  91 ekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlGikPLYyaseqgkllf 159
                                                      t sDtEVi+++y+++g +++++L+GmF f+++d k++++f aRDr+G+kP++y+ +++k++f
  lcl|NCBI__GCF_000092245.1:WP_013133950.1  82 L---LCSTSSDTEVIIRLYQKYGIDFLNKLNGMFSFVIFDLKQEKYFCARDRYGKKPFFYYFKDNKFIF 147
                                               4...599************************************************************** PP

                                 TIGR01536 160 aSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakal...dgeekleeywevekee 225
                                               +S iK+++++  ++++l+k al+++l++ ++ ++ t+++++++le+++++   ++e  +++y+++++ +
  lcl|NCBI__GCF_000092245.1:WP_013133950.1 148 SSSIKSIIKILGFTPKLNKVALSQYLQYFVSLNDMTFYNDINKLEASSYMllsSNELFIKKYYKINTYK 216
                                               *****************************99******************998655566677******** PP

                                 TIGR01536 226 vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeaksevktFsigfedskdld 294
                                               +  +e+++ ++++ell ++v++rlv+dv+vg+llSGG+DSs+++++  +   ++++tFs+g+ d+ +++
  lcl|NCBI__GCF_000092245.1:WP_013133950.1 217 KVVDEKQALNDIEELLFKSVESRLVGDVEVGSLLSGGIDSSFISSLYTNITGKRINTFSVGYSDHISYS 285
                                               ********************************************************************* PP

                                 TIGR01536 295 eskaarkvadelgtehkevliseeevlkeleevilaleeptairasiplyllsklarekgvkVvLsGeG 363
                                               e ++a+ v++++ + h+ +++s++++++ ++evi aleep a++a++ply l+kl+++kg+kVvLsGeG
  lcl|NCBI__GCF_000092245.1:WP_013133950.1 286 ELDYASLVSKDINSIHHPLEVSRNDFIDVFDEVIDALEEPHADSAAFPLYCLTKLINKKGIKVVLSGEG 354
                                               ********************************************************************* PP

                                 TIGR01536 364 aDElfgGYeyfreakaeeale..............lpeaselaekklllqaklakeselke...ll.ka 414
                                               +DElf GY+ + ++ +  +++              ++ +++ +++++ l++ +++e+  +    +    
  lcl|NCBI__GCF_000092245.1:WP_013133950.1 355 SDELFLGYDNYSKFLKYYKFKeslsadqdgflkdiISALQNNTKESEYLRRVVTDENIYNSfgeIYtTI 423
                                               *************99999999776666666655543333333333333333333333222200022022 PP

                                 TIGR01536 415 kleeelkekeelkkelkeeseleellrldlelllsdllrak.DrvsmahslEvRvPflDkelvelalsi 482
                                               + ++  k+  + k+e +++  ++ + + dl+ +l + l+ k Dr+sma+s+EvR PflD +lv++ +s+
  lcl|NCBI__GCF_000092245.1:WP_013133950.1 424 QKKRLFKRLPTFKQEKAKKDPVDWMSYIDLKIWLGQSLLSKvDRISMANSIEVRTPFLDFRLVDYLFSV 492
                                               22333333333444444448999********************************************** PP

                                 TIGR01536 483 ppelklrdgkeKvlLreaaeellPeeileRkKeaf 517
                                               +++lk+ d ++K+lL+++a +++Pe+i +R K++f
  lcl|NCBI__GCF_000092245.1:WP_013133950.1 493 DTKLKTGD-TNKYLLKKIASKYIPEKIINRTKKGF 526
                                               **999875.68*********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (593 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: 00:00:00.02
# Mc/sec: 12.57
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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