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 Putative asparagine synthetase [glutamine-hydrolyzing] 2; EC 6.3.5.4 (uncharacterized)
to candidate WP_013461234.1 SULKU_RS11960 asparagine synthase (glutamine-hydrolyzing)

Query= curated2:Q58456
         (515 letters)



>NCBI__GCF_000183725.1:WP_013461234.1
          Length = 601

 Score =  182 bits (462), Expect = 3e-50
 Identities = 127/395 (32%), Positives = 197/395 (49%), Gaps = 38/395 (9%)

Query: 1   MCGINGII-RFGKEVIKEEINKMNKAIKHRGPDDEGIFIYNFKNYSIGLGHVRLAILDLS 59
           MCG+ GII  +     +E +    K ++HRG D  G+   N    ++ L H RL+I D+ 
Sbjct: 1   MCGVFGIIGHYSPHKAREAL----KTLQHRGRDYCGVVEQN----TLFLAHQRLSITDVH 52

Query: 60  EKGHQPMGYNVDEDKIIYRDDELDRADIIIVYNGEIYNYLELKEKFN-LETETGTDTEVI 118
            + HQPM           R D+L     +I +NGEIYN+  L+E+   L+ ET +DTEV+
Sbjct: 53  PRSHQPM-----------RRDKL-----LISFNGEIYNHARLREQLTGLKWETSSDTEVV 96

Query: 119 LKLYNKLGFDCVKEFNGMWAFCIFDKKKGLIFCSRDRLGVKPFYYYWDGNEFIFSSELKG 178
           L  Y + G  CV+   GM+AF + D  K   +  RDR G KP +Y+     F+F SE+K 
Sbjct: 97  LAAYERWGIRCVEYLEGMFAFALIDGDK--CYLVRDRFGKKPLFYHQSNEAFVFGSEIK- 153

Query: 179 ILAVKEINKKENINKDAVELYFALGFIPSPYSIYKNTFKLEARQNLIFDLDKREIRKYY- 237
             A+K       +N +A+  Y +      P++ YK   KLE+ + L  +  K    +YY 
Sbjct: 154 --AIKPFLSSVYMNDEALHSYLSFLAPTPPHTFYKGIEKLESGEWLCAEQGKITKHRYYN 211

Query: 238 YWELPDYKPIYDKKKLIEEGKKLLYDAVKIRMRSDVPVGAFLSGGLDSSTVVGVMREFTD 297
             + PD   I      +   ++ L+ A+ +R+ ++VP+ A LSGGLDS+ +  +      
Sbjct: 212 LLDTPD-SSITGNSDALYRIEEELHRAIAVRLDTEVPIAALLSGGLDSAMICAIAAR--Q 268

Query: 298 LSKLHTFSIGFE--GKYDETPYIKIVVDYFKTQHHHYYFKERDFEELIDKYSWIYDEPFG 355
             KL  F++G+     YDE     +   Y    H      + DF+E +D+     DEP  
Sbjct: 269 GKKLPVFTLGYNEYDAYDERKNAAMTAKYLGLDHTEVIISQNDFDEHLDELLTHMDEPLN 328

Query: 356 DYSGFPTY-KVSEMARKFVTVVLSGDGGDEVFGGY 389
           D +  P Y  + ++  +   VVLSG+G DE+F GY
Sbjct: 329 DPAALPLYLLMKKIGAEGYKVVLSGEGSDELFLGY 363


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: 825
Number of extensions: 54
Number of successful extensions: 8
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: 601
Length adjustment: 36
Effective length of query: 479
Effective length of database: 565
Effective search space:   270635
Effective search space used:   270635
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_013461234.1 SULKU_RS11960 (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.12478.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     2e-130  422.2   0.0   2.2e-130  422.0   0.0    1.0  1  lcl|NCBI__GCF_000183725.1:WP_013461234.1  SULKU_RS11960 asparagine synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000183725.1:WP_013461234.1  SULKU_RS11960 asparagine synthase (glutamine-hydrolyzing)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  422.0   0.0  2.2e-130  2.2e-130       1     517 []       2     538 ..       2     538 .. 0.86

  Alignments for each domain:
  == domain 1  score: 422.0 bits;  conditional E-value: 2.2e-130
                                 TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsne 68 
                                               Cg++gi+ ++       ++++e l+tl+hRG D  gv +   ++   l+h+RL+i+d++   +QP++ +
  lcl|NCBI__GCF_000183725.1:WP_013461234.1   2 CGVFGIIGHYSP-----HKAREALKTLQHRGRDYCGVVE---QNTLFLAHQRLSITDVHPRsHQPMRRD 62 
                                               *********886.....445666889**********744...5899*************999******9 PP

                                 TIGR01536  69 kevvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelf 137
                                               k  +i fnGEIYNh  Lre+l   G ++et sDtEV+Laaye wg ++ve+LeGmFAfal+d   ++ +
  lcl|NCBI__GCF_000183725.1:WP_013461234.1  63 K-LLISFNGEIYNHARLREQLT--GLKWETSSDTEVVLAAYERWGIRCVEYLEGMFAFALIDG--DKCY 126
                                               9.79*****************9..89*************************************..9*** PP

                                 TIGR01536 138 laRDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepa 206
                                               l+RDr+G+kPL+y + +++++f+SEiKa+ ++    + +++eal+++l++   ++++t++k++++le +
  lcl|NCBI__GCF_000183725.1:WP_013461234.1 127 LVRDRFGKKPLFYHQSNEAFVFGSEIKAIKPFL-SSVYMNDEALHSYLSFLAPTPPHTFYKGIEKLESG 194
                                               *********************************.699**************999*************** PP

                                 TIGR01536 207 kal...dgeekleeywevekee..vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaa 270
                                               + l   +g+ ++++y+++ ++     +  +++  +++e l++a++ rl ++vp+++llSGGlDS +++a
  lcl|NCBI__GCF_000183725.1:WP_013461234.1 195 EWLcaeQGKITKHRYYNLLDTPdsSITGNSDALYRIEEELHRAIAVRLDTEVPIAALLSGGLDSAMICA 263
                                               *9997666677777998877665644557788999********************************** PP

                                 TIGR01536 271 iakkeaksevktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptaira 339
                                               ia+++ k ++ +F++g+++ +++de k a+ +a++lg++h+ev+is++++ ++l+e++ +++ep++++a
  lcl|NCBI__GCF_000183725.1:WP_013461234.1 264 IAARQGK-KLPVFTLGYNEYDAYDERKNAAMTAKYLGLDHTEVIISQNDFDEHLDELLTHMDEPLNDPA 331
                                               *****88.8************************************************************ PP

                                 TIGR01536 340 siplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeeale.............lpeaselaekk 395
                                               + plyll+k++ ++g+kVvLsGeG+DElf GY  ++e+   e++                         
  lcl|NCBI__GCF_000183725.1:WP_013461234.1 332 ALPLYLLMKKIGAEGYKVVLSGEGSDELFLGYRQYFEYLDIEKAAslhhknwlkkyfhS---------- 390
                                               ***********************************999888877745554444444330.......... PP

                                 TIGR01536 396 l....................llqaklakeselkellkakleeelkek.....eelkkelkeeseleel 439
                                               +                    +++   ++  ++++l++++++++ + +     +++++++++e+     
  lcl|NCBI__GCF_000183725.1:WP_013461234.1 391 HfsmnrewewykrifddtllfRTSGDKFTDLQQNKLFRRNVRDNESLRflesyRRMFEQSAHEHPSVWY 459
                                               034445555666667777777444444444455555555555544433000004444444444555556 PP

                                 TIGR01536 440 lrldlelllsdllrak.DrvsmahslEvRvPflDkelvelalsippelklrdgkeKvlLreaaeellPe 507
                                                  dl+l++ +  + k Drvsmah +E+R PflD+ l+e++ls++p+l++ +g +K lL+++a+++l +
  lcl|NCBI__GCF_000183725.1:WP_013461234.1 460 SMIDLKLFVGEHFLTKlDRVSMAHTIEARTPFLDHILAETVLSVDPSLRIGNGGTKPLLKQIARNYLSD 528
                                               67789999999999999**************************************************** PP

                                 TIGR01536 508 eileRkKeaf 517
                                               ei +RkK++f
  lcl|NCBI__GCF_000183725.1:WP_013461234.1 529 EIITRKKKGF 538
                                               ********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (601 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 13.93
//
[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