Alignments for a candidate for asnB in Sulfuricurvum kujiense DSM 16994

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Sulfuricurvum kujiense DSM 16994

Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate WP_013461241.1 SULKU_RS11995 asparagine synthase (glutamine-hydrolyzing)

Query= CharProtDB::CH_005185
         (632 letters)



>NCBI__GCF_000183725.1:WP_013461241.1
          Length = 552

 Score =  224 bits (570), Expect = 1e-62
 Identities = 169/569 (29%), Positives = 274/569 (48%), Gaps = 44/569 (7%)

Query: 1   MCGFVGVFNKHPLAQTADQEELIKQMNQMIVHRGPDSDGYFHDEHVGFGFRRLSIIDVEN 60
           MCG  G  +K+   +  + ++++++M    VHRGPD  G    +    G  RLSIID   
Sbjct: 1   MCGIAGFISKN---KDYNAQKIVQEMLDRGVHRGPDQSGLATYQDTTIGMVRLSIIDTVE 57

Query: 61  GGQPLSYEDETYWIIFNGEIYNYIELREELEAKGYTFNTDSDTEVLLATYRHYKEEAASK 120
              P       + I++NGEIYN+ E+R+ L  K YTF T+SDTE  + ++      A  +
Sbjct: 58  HTIPYEDSSGNFAIVYNGEIYNHQEIRKNL--KYYTFLTNSDTETAMVSFIDKGINAFKE 115

Query: 121 LRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTINDQVYFASERKSLMVAQNDIEIDKEA 180
             GM+AF + +K  +  Y  RD  G KPLYY    D   FASE KSLM        DK  
Sbjct: 116 YNGMYAFALHDKKKNETYIVRDKVGEKPLYYVKTKDFFAFASEIKSLMGLVEPKLNDKAV 175

Query: 181 LQQYMSFQFVPEPSTLDAHVKKVEPGSQFTIRPDGDITFKTYFKANFKPVQT--EEDKLV 238
              Y +++F     TL   +  +EPG    ++ +   T K+Y+K    P+     E K++
Sbjct: 176 --SYRAYEFTTGKETLFKDIYLLEPGEYIHVK-NNKATIKSYWKIWDHPIDVPDNEAKIL 232

Query: 239 KEVRDAIYDSVNVHMRSDV-PVGSFLSGGIDSSFIVSVAKEFHPSLKTFSVGFEQQGFSE 297
             + + + DS+ +  ++     G+F+SGGIDSS +  +AK  H     ++  ++   F+E
Sbjct: 233 SSLAELVEDSILLRTQNSAHAFGAFVSGGIDSSLVACIAKPDH----LYTAHYDYSDFNE 288

Query: 298 VDVAKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADPAAIPLYFVAKEAKKHVT 357
           +D AK  A  L  + I    + ++++    +I +H D P    +      + + ++  + 
Sbjct: 289 LDYAKLVAKQLKKKLIIVEPTKDDFLRTQEQIAYHLDTPCTWTSFTLWALMERISQDGLK 348

Query: 358 VALSGEGADELFGGYNIYREPLSLKPFERIPSGLKKMLLHVAAVMPEGMRGKSLLERGCT 417
           V L+G+GADE+FGGY+ Y     L   E+I         H    M E      L+ R   
Sbjct: 349 VMLTGDGADEVFGGYHRYH---LLHHDEQI---------HTLEAMKE---YSYLINRYYG 393

Query: 418 PLQDRYIGNAKIFEESVKKQLLKHYNPNLSYRDVTKTYFTESSSYSDINKMQYVDIHTWM 477
              +RY       E     ++LK  N ++ +      YF E      ++ M   D ++ M
Sbjct: 394 SPVERYTKLVNRSENPYDTKVLKFLNESIGF------YF-EKMQKDVVHAMGLNDFYSTM 446

Query: 478 RGDILLKADKMTMANSLELRVPFLDKVVFDVASKIPDELKTKNGTTKYLLRKAAEGIVPE 537
           +  +L  +D+++MA S+E R PFLD  +   A  +P + K KNG TK+ L++ A   +P+
Sbjct: 447 Q-VLLQMSDRVSMAFSIENRSPFLDYRLIQFAFSMPSKYKIKNGITKWALKEVARKFIPK 505

Query: 538 HVLNR-KKLGFPVPIRHWLKNEMNEWVRN 565
            + +R  K GF  P+  W      EW +N
Sbjct: 506 EICDRVDKRGFSAPVNKWF-----EWDKN 529


Lambda     K      H
   0.319    0.136    0.403 

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: 875
Number of extensions: 51
Number of successful extensions: 6
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: 632
Length of database: 552
Length adjustment: 37
Effective length of query: 595
Effective length of database: 515
Effective search space:   306425
Effective search space used:   306425
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 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate WP_013461241.1 SULKU_RS11995 (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.4802.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-120  389.6   0.9   1.6e-120  389.4   0.9    1.0  1  lcl|NCBI__GCF_000183725.1:WP_013461241.1  SULKU_RS11995 asparagine synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000183725.1:WP_013461241.1  SULKU_RS11995 asparagine synthase (glutamine-hydrolyzing)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  389.4   0.9  1.6e-120  1.6e-120       1     517 []       2     516 ..       2     516 .. 0.87

  Alignments for each domain:
  == domain 1  score: 389.4 bits;  conditional E-value: 1.6e-120
                                 TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsnek 69 
                                               Cgiag++ ++++ + + + ++eml++  hRGPD++g+  +   ++  +g +RL+iid  e + P ++ +
  lcl|NCBI__GCF_000183725.1:WP_013461241.1   2 CGIAGFISKNKDYNAQ-KIVQEMLDRGVHRGPDQSGLATY---QDTTIGMVRLSIIDTVEHTIPYEDSS 66 
                                               *********9988775.9******************7555...899*********************** PP

                                 TIGR01536  70 .evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelf 137
                                                + +iv+nGEIYNh+e+r++l+   y+F t+sDtE  + ++   g +++++ +Gm+Afal+d+kk+e +
  lcl|NCBI__GCF_000183725.1:WP_013461241.1  67 gNFAIVYNGEIYNHQEIRKNLK--YYTFLTNSDTETAMVSFIDKGINAFKEYNGMYAFALHDKKKNETY 133
                                               999******************9..47******************************************* PP

                                 TIGR01536 138 laRDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepa 206
                                               ++RD++G kPLYy ++++ ++faSEiK+l+ l   +++l+++a++ + ++++++ ++tlfk+++ lep+
  lcl|NCBI__GCF_000183725.1:WP_013461241.1 134 IVRDKVGEKPLYYVKTKDFFAFASEIKSLMGLV--EPKLNDKAVS-YRAYEFTTGKETLFKDIYLLEPG 199
                                               *******************************98..6777776654.5555556899************* PP

                                 TIGR01536 207 kal...dgeekleeywevekee..vkeseeelveelrelledavkkrlv.advpvgvllSGGlDSslva 269
                                               ++    ++++++++yw++ ++   v ++e +  ++l el+ed++  r   +    g+++SGG+DSslva
  lcl|NCBI__GCF_000183725.1:WP_013461241.1 200 EYIhvkNNKATIKSYWKIWDHPidVPDNEAKILSSLAELVEDSILLRTQnSAHAFGAFVSGGIDSSLVA 268
                                               *9977777777788****99986677889999***************98788999************** PP

                                 TIGR01536 270 aiakkeaksevktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptair 338
                                               +iak       ++++ +++  +d++e ++a+ va++l  ++  v+ +++++l   e++ ++l+ p +  
  lcl|NCBI__GCF_000183725.1:WP_013461241.1 269 CIAKPD-----HLYTAHYD-YSDFNELDYAKLVAKQLKKKLIIVEPTKDDFLRTQEQIAYHLDTPCTW- 330
                                               ****99.....88*****9.9*********************************************65. PP

                                 TIGR01536 339 asiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeealelpeaselaekklllqaklak... 404
                                                s++l++l+++++++g+kV+L+G+GaDE+fgGY++++  + +e++++ ea++  e + l+++++ +   
  lcl|NCBI__GCF_000183725.1:WP_013461241.1 331 TSFTLWALMERISQDGLKVMLTGDGADEVFGGYHRYHLLHHDEQIHTLEAMK--EYSYLINRYYGSpve 397
                                               6789*****************************************9555554..333333333322000 PP

                                 TIGR01536 405 .eselkellkakleeelkekeelkkelkee..........seleellrldlelllsdllrakDrvsmah 462
                                                 ++l +  +  +++++   + l++    +            ++++  +d+   ++ ll+++Drvsma 
  lcl|NCBI__GCF_000183725.1:WP_013461241.1 398 rYTKLVNRSENPYDTKV--LKFLNE----SigfyfekmqkDVVHAMGLNDFYSTMQVLLQMSDRVSMAF 460
                                               02222222222222222..222222....2222243344467788888999****************** PP

                                 TIGR01536 463 slEvRvPflDkelvelalsippelklrdgkeKvlLreaaeellPeeileR.kKeaf 517
                                               s+E R PflD +l+++a+s+p ++k+++g +K+ L+e+a++ +P+ei +R +K++f
  lcl|NCBI__GCF_000183725.1:WP_013461241.1 461 SIENRSPFLDYRLIQFAFSMPSKYKIKNGITKWALKEVARKFIPKEICDRvDKRGF 516
                                               *****************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (552 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: 11.90
//
[ok]

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

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