Alignments for a candidate for asnB in Clostridium kluyveri DSM 555

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Clostridium kluyveri DSM 555

Align asparagine synthase (glutamine-hydrolysing) (EC 6.3.5.4) (characterized)
to candidate WP_012102652.1 CKL_RS11315 asparagine synthase B

Query= BRENDA::B3KYI2
         (570 letters)



>NCBI__GCF_000016505.1:WP_012102652.1
          Length = 529

 Score =  320 bits (821), Expect = 7e-92
 Identities = 204/519 (39%), Positives = 298/519 (57%), Gaps = 33/519 (6%)

Query: 1   MCGILAVFGCVDHSQAKRARIIELSRRLRHRGPDWSGLHCHDDCFLAHQRLAIVDPT-SG 59
           MC I+    C   +  K  +  E  +R   RGPD   +       L  QRL+I+D + SG
Sbjct: 1   MCTIM----CYTGTDMKHGKFAEALQRTESRGPDMMEILTLPSGILGFQRLSIMDLSFSG 56

Query: 60  DQPLYNEDKTVIVTVNGEIYNHKQLRQKL--SSHKFRTGSDCEVIAHLYEEYGEEFVNML 117
            QP   +    I   NGEIY  +++++ L    HKF + SDCE++  +Y EYG +  + L
Sbjct: 57  MQPFTRKMDAAIC--NGEIYGFREIKKDLIKKGHKFISDSDCEILLPMYYEYGLDMFSKL 114

Query: 118 DGMFAFVLLDTRDKSFIAARDAIGITPLYLGWGHDGSTWFASEMKALSDDCERFMSFPPG 177
           D  FA V+ D +  S+IAARD IGI PL+ G+   G   FASE K L    ++ M FPPG
Sbjct: 115 DAEFATVIYDGKKDSYIAARDPIGIRPLFYGYSESGKIIFASEAKNLIGLTDKIMPFPPG 174

Query: 178 HIYSSKQGGLRRWYNPHWFSEDIPSTPYDPIL--LRETFERAVVKRMMTDVPFGVLLSGG 235
           H Y+   G    + +      D      D I   + +    AV KRM  D P G LLSGG
Sbjct: 175 HYYTD--GKFTCYCDIAAKESDYCKDDLDVIFNKIHDKLVAAVKKRMDADAPVGFLLSGG 232

Query: 236 LDSSLVASVVNRYLKESEAARQWGSQLHTFCIGL-KGSPDLKAAKEVADYLGTRHHELYF 294
           LDSSLV ++  +   +          + TF +G+ + + DLK AKEVADY+ + H  +Y 
Sbjct: 233 LDSSLVCAIAQKMNPKKP--------IRTFSVGMTEDAIDLKYAKEVADYIHSDHTVVYM 284

Query: 295 TVQEGIDALEEVIYHIETYDVTTIRASTPMFLMSRKIKALG-VKMVLSGEGSDEIFGGYL 353
           T +E +++L+EVI  + TYD+TTIRAS  M+L+ +KI  +  ++++L+GE SDE+F GY 
Sbjct: 285 TKEEVLNSLDEVIKILGTYDITTIRASMGMYLICKKIHEISDIRVLLTGEISDELF-GYK 343

Query: 354 YFHKAPNKKEFHEETCRKIKALHLYDCLRANKSTAAWGVEARVPFLDKEFIDVAMSIDPE 413
           Y   APN +EF +E+ ++I+ L++YD LRA++  ++  +EARVPF D +F+   MSIDPE
Sbjct: 344 YTDFAPNAEEFQKESQKRIRELYMYDVLRADRCISSNSLEARVPFGDLDFVKYVMSIDPE 403

Query: 414 WKMIRRDLGRIEKWVLRNAFDDEKNPYLPKHILYRQKEQFSDGVGYSWIDALKDHADKQV 473
            K+ + ++G   K++LR +F+     YLP  ILYR+K  FSD VG+S +D LK++A+   
Sbjct: 404 KKLNKYNMG---KYLLRRSFE---GSYLPHDILYREKAAFSDAVGHSMVDYLKEYAETFY 457

Query: 474 PDATM--LAANFIYPENTPTTKEGYLYRTIFEKFFPKNA 510
            D     +  N+ Y    P TKE  LYR IFEK++   A
Sbjct: 458 SDEEFEKICENYEY-HARPFTKESLLYREIFEKYYSGQA 495


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: 719
Number of extensions: 44
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: 570
Length of database: 529
Length adjustment: 36
Effective length of query: 534
Effective length of database: 493
Effective search space:   263262
Effective search space used:   263262
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_012102652.1 CKL_RS11315 (asparagine synthase B)
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.9203.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.1e-118  382.5   0.6    3.1e-93  299.4   0.3    3.0  2  lcl|NCBI__GCF_000016505.1:WP_012102652.1  CKL_RS11315 asparagine synthase 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016505.1:WP_012102652.1  CKL_RS11315 asparagine synthase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  299.4   0.3   3.1e-93   3.1e-93      18     384 ..      15     355 ..       2     363 .. 0.88
   2 !   75.3   0.0   2.6e-25   2.6e-25     438     517 .]     357     437 ..     355     437 .. 0.96

  Alignments for each domain:
  == domain 1  score: 299.4 bits;  conditional E-value: 3.1e-93
                                 TIGR01536  18 eaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsnekevvivfnGEIYNheeL 85 
                                                + +e l++ + RGPD   +         ilg++RL+i+dls   +QP+  +   + ++nGEIY ++e+
  lcl|NCBI__GCF_000016505.1:WP_012102652.1  15 GKFAEALQRTESRGPDMMEILTL---PSGILGFQRLSIMDLSFSgMQPFTRKMD-AAICNGEIYGFREI 79 
                                               34555577899*******98766...699************9766******995.7899********** PP

                                 TIGR01536  86 reeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlGikPLYyase. 153
                                               +++l++kG++F ++sD+E++L  y e+g +++++L+++FA +++d kk+ +++aRD++Gi+PL+y++  
  lcl|NCBI__GCF_000016505.1:WP_012102652.1  80 KKDLIKKGHKFISDSDCEILLPMYYEYGLDMFSKLDAEFATVIYDGKKDSYIAARDPIGIRPLFYGYSe 148
                                               ******************************************************************998 PP

                                 TIGR01536 154 qgkllfaSEiKallalk.eikaeldkealaelltlqlvptektlfkevkelepakaldgeekleeywev 221
                                               +gk++faSE+K l+ l  +i +++++++++++    +         ++   e        ++ +     
  lcl|NCBI__GCF_000016505.1:WP_012102652.1 149 SGKIIFASEAKNLIGLTdKIMPFPPGHYYTDGKFTCY--------CDIAAKES-------DYCK----- 197
                                               9****************9************9988773........23322222.......2222..... PP

                                 TIGR01536 222 ekeevkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeak.sevktFsigfed 289
                                                     ++++   +++ ++l +avkkr+ ad+pvg llSGGlDSslv+aia+k  + ++++tFs+g++ 
  lcl|NCBI__GCF_000016505.1:WP_012102652.1 198 ------DDLDVIFNKIHDKLVAAVKKRMDADAPVGFLLSGGLDSSLVCAIAQKMNPkKPIRTFSVGMT- 259
                                               ......345556789***************************************9989**********. PP

                                 TIGR01536 290 skdldeskaarkvadelgtehkevliseeevlkeleevilale..eptairasiplyllsklarek.gv 355
                                               ++++d  k+a++vad++ ++h+ v++++eevl+ l+evi +l   ++t+iras+++yl++k+++e  ++
  lcl|NCBI__GCF_000016505.1:WP_012102652.1 260 EDAID-LKYAKEVADYIHSDHTVVYMTKEEVLNSLDEVIKILGtyDITTIRASMGMYLICKKIHEIsDI 327
                                               44444.56**********************************99********************988** PP

                                 TIGR01536 356 kVvLsGeGaDElfgGYeyfreakaeeale 384
                                               +V+L+Ge +DElfg Y+y + a+++e+++
  lcl|NCBI__GCF_000016505.1:WP_012102652.1 328 RVLLTGEISDELFG-YKYTDFAPNAEEFQ 355
                                               *************7.***********998 PP

  == domain 2  score: 75.3 bits;  conditional E-value: 2.6e-25
                                 TIGR01536 438 ellrldlelllsdllrakDrvsmahslEvRvPflDkelvelalsippelklr.dgkeKvlLreaaee.l 504
                                               e +++  el+++d+lra+ r+ + +slE+RvPf D ++v++++si+pe+kl+  ++ K+lLr+ +e+ +
  lcl|NCBI__GCF_000016505.1:WP_012102652.1 357 ESQKRIRELYMYDVLRAD-RCISSNSLEARVPFGDLDFVKYVMSIDPEKKLNkYNMGKYLLRRSFEGsY 424
                                               67888899********99.*********************************99*************** PP

                                 TIGR01536 505 lPeeileRkKeaf 517
                                               lP++il+R+K+af
  lcl|NCBI__GCF_000016505.1:WP_012102652.1 425 LPHDILYREKAAF 437
                                               ***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (529 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: 0.08u 0.01s 00:00:00.09 Elapsed: 00:00:00.08
# Mc/sec: 3.12
//
[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