Alignments for a candidate for asnB in Sinorhizobium fredii NGR234

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Sinorhizobium fredii NGR234

Align Putative asparagine synthetase [glutamine-hydrolyzing]; EC 6.3.5.4 (characterized)
to candidate YP_002823396.1 NGR_b11900 asparagine synthase

Query= SwissProt::P64248
         (652 letters)



>NCBI__GCF_000018545.1:YP_002823396.1
          Length = 653

 Score =  265 bits (676), Expect = 6e-75
 Identities = 210/648 (32%), Positives = 300/648 (46%), Gaps = 55/648 (8%)

Query: 21  DAASAIARASHLMRHRGPDESGTWHAVDGASGGVVFGFNRLSIIDIAHSH-QPLRWGPPE 79
           D A  + R +  + HRGPD S TW   DG  G    G  RLSIID++ +  QP+      
Sbjct: 17  DVAQILTRMTDALAHRGPDASATWLDRDGRVG---LGHRRLSIIDLSPTGAQPMH----S 69

Query: 80  APDRYVLVFNGEIYNYLELRDELRTQHGAVFATDGDGEAILAGYHHWGTE-VLQRLRGMF 138
           +  RY +VFNGE+Y +L LR  L  Q GA F    D E +L     +G    LQR  GMF
Sbjct: 70  SSGRYSIVFNGEVYGFLRLRAALEEQ-GARFRGHSDTEVLLEAIETYGLAGALQRCNGMF 128

Query: 139 AFALWDTVTRELFCARDPFGIKPLFIATGAGGTAVASEKKCLLDLVELVGFDTEIDHRAL 198
           AFAL+D+ TR++  ARD  G KPL+I     G A  SE K +           E+D  A 
Sbjct: 129 AFALYDSATRQIIFARDRIGKKPLYIGVSKRGVAFGSELKSIRAHPSFRS--VEVDPEAS 186

Query: 199 QHYTVLQYVPEPETLHRGVRRLESGCFARIRADQLAPV-------ITRYFVPRFAASPIT 251
             +    YVP P +++RG+ +L  G +  +  D            +  Y+    AA    
Sbjct: 187 TLFLRYGYVPTPYSIYRGIFKLPHGSWLSLSVDTPPASASAALGGVKSYWDAFEAAERGY 246

Query: 252 NDN----DQARYDEITAVLEDSVAKHMRADVTVGAFLSGGIDSTAIAALAIR-HNPRLIT 306
            +     D+A  D + A L+ +V++ + +DV VGA LS G+DS+ ++A+       R+ T
Sbjct: 247 AERIECPDEA-LDALDAELKRAVSERLVSDVPVGALLSSGVDSSLVSAVMQEVSTSRVKT 305

Query: 307 FTTGFEREGFSEIDVAVASAEAIGARHIAKVVSADEFVAALPEIVWYLDEPVADPALVPL 366
           +T  F  E ++E D+A   A  +G  H       D  +  + E+    DEP ADP+ +P 
Sbjct: 306 YTVRFLEEQYNEADLASGIARQLGTDHTEITAEPDTALRVVTELPDVYDEPFADPSQIPT 365

Query: 367 FFVAREARKHVKVVLSGEGADELFGGYTIYREPLSLRPFDYLPKPLRRSMGKVSKPLPE- 425
             V++ AR+ V V LSG+G DE FGGY  YR+ L+   FD L +       + ++  P  
Sbjct: 366 LLVSKLARRTVTVALSGDGGDEFFGGYKRYRQMLA---FDRLARKTPAVALRAARHAPHW 422

Query: 426 --GMRGKSLLHRGSLTLEERYYGNARSFSGAQLREV------LPGFRPDWTH-------- 469
                  +  H    +L++   G  R    A+L E+         FR  W+H        
Sbjct: 423 ALEFAAAAARHARPSSLQDEVTGK-RLRRLAELLEIEDPDARYLDFRSLWSHPAEVVFGG 481

Query: 470 ----TDVTAPVYAESAGWDPVARMQHIDLFTWLRGDILVKADKITMANSLELRVPFLDPE 525
               T +TA       G   V RM + D+  +L  DILVK D+ +MA  LE+R P LD  
Sbjct: 482 AEPPTAMTAKRIPACLG--AVDRMMYSDMVDYLPDDILVKMDRASMAVGLEMRAPLLDYR 539

Query: 526 VFAVASRLPAGAKITRTTTKYALRRALEPIVPAHVLHRPKLGFPVPIRHWLRAGELLEWA 585
              +A R P          K ALR  L   +P   ++  K GF VP+  WLR G L  WA
Sbjct: 540 FVELAWRAPRALCFAEAPGKPALRALLSRRLPEQFINLSKRGFGVPVNAWLR-GPLRAWA 598

Query: 586 YATVGSS--QAGHLVDIAAVYRMLDEHRCGSSDHSRRLWTMLIFMLWH 631
              +  S  Q   +     +      H  G  D   +LW +L+F LWH
Sbjct: 599 EEMLSPSRLQRDGIFRADPIVSRWKAHLAGRRDWGPQLWAVLMFNLWH 646


Lambda     K      H
   0.323    0.138    0.428 

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: 1033
Number of extensions: 66
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 652
Length of database: 653
Length adjustment: 38
Effective length of query: 614
Effective length of database: 615
Effective search space:   377610
Effective search space used:   377610
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (25.4 bits)

Align candidate YP_002823396.1 NGR_b11900 (asparagine synthase)
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.11770.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.7e-134  434.9   0.0   3.5e-134  434.5   0.0    1.1  1  lcl|NCBI__GCF_000018545.1:YP_002823396.1  NGR_b11900 asparagine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000018545.1:YP_002823396.1  NGR_b11900 asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  434.5   0.0  3.5e-134  3.5e-134       1     517 []       2     582 ..       2     582 .. 0.86

  Alignments for each domain:
  == domain 1  score: 434.5 bits;  conditional E-value: 3.5e-134
                                 TIGR01536   1 Cgiagivdlkakake.eeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsn 67 
                                               Cgiag++d+ +  ++   + + +m+++lahRGPDa+++w d ++ +++lghrRL+iidls   aQP+++
  lcl|NCBI__GCF_000018545.1:YP_002823396.1   2 CGIAGLIDYAQRGRDdVAQILTRMTDALAHRGPDASATWLD-RDGRVGLGHRRLSIIDLSPTgAQPMHS 69 
                                               *********998888777999********************.79****************988****** PP

                                 TIGR01536  68 ek.evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewg.eelverLeGmFAfalwdekkg 134
                                                + ++ ivfnGE+Y +  Lr+ lee+G +F+++sDtEV+L+a+e++g   +++r +GmFAfal+d++++
  lcl|NCBI__GCF_000018545.1:YP_002823396.1  70 SSgRYSIVFNGEVYGFLRLRAALEEQGARFRGHSDTEVLLEAIETYGlAGALQRCNGMFAFALYDSATR 138
                                               ********************************************************************* PP

                                 TIGR01536 135 elflaRDrlGikPLYyaseqgkllfaSEiKallalk.eikaeldkealaelltlqlvptektlfkevke 202
                                               +++ aRDr+G+kPLY +  +  ++f+SE+K++ a++    +e+d ea + +l + +vpt+ ++++++++
  lcl|NCBI__GCF_000018545.1:YP_002823396.1 139 QIIFARDRIGKKPLYIGVSKRGVAFGSELKSIRAHPsFRSVEVDPEASTLFLRYGYVPTPYSIYRGIFK 207
                                               *******************9****************4445789999999999999************** PP

                                 TIGR01536 203 lepakal............dgeeklee....ywevekee......vkeseeelveelrelledavkkrl 249
                                               l++++ l                        yw++ + +      + e  +e+ + l+  l++av +rl
  lcl|NCBI__GCF_000018545.1:YP_002823396.1 208 LPHGSWLslsvdtppasasAAL----GgvksYWDAFEAAergyaeRIECPDEALDALDAELKRAVSERL 272
                                               *****99999998776443333....1455699876666578774444457899*************** PP

                                 TIGR01536 250 vadvpvgvllSGGlDSslvaaiakkeaksevktFsigfedskdldeskaarkvadelgtehkevlisee 318
                                               v+dvpvg+llS+G+DSslv+a++++ + s+vkt++++f  +++++e++ a+ +a++lgt+h+e++ +++
  lcl|NCBI__GCF_000018545.1:YP_002823396.1 273 VSDVPVGALLSSGVDSSLVSAVMQEVSTSRVKTYTVRFL-EEQYNEADLASGIARQLGTDHTEITAEPD 340
                                               ***************************************.9**************************** PP

                                 TIGR01536 319 evlkeleevilaleeptairasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeeale... 384
                                               ++l  + e+  + +ep+a++++ip++l+sklar+  v+V+LsG+G+DE fgGY+++r++ a  +l    
  lcl|NCBI__GCF_000018545.1:YP_002823396.1 341 TALRVVTELPDVYDEPFADPSQIPTLLVSKLARRT-VTVALSGDGGDEFFGGYKRYRQMLAFDRLArkt 408
                                               ***********************************.***********************9988887788 PP

                                 TIGR01536 385 ..................lpeaselaekkl.....llqaklakeselkellkakleeelkekeelkkel 430
                                                                                  +  ++l++e++ k+l +     e++  ++   ++
  lcl|NCBI__GCF_000018545.1:YP_002823396.1 409 pavalraarhaphwalefA----------AaaarhARPSSLQDEVTGKRLRRLAELLEIEDPDARYLDF 467
                                               8877766666655444431..........0222232222333333333333332222222222222222 PP

                                 TIGR01536 431 kee...........................seleellrldlelllsdllrak.DrvsmahslEvRvPfl 471
                                                +                             ++++++++d+  +l+d++++k Dr+sma +lE+R+P+l
  lcl|NCBI__GCF_000018545.1:YP_002823396.1 468 RSLwshpaevvfggaepptamtakripaclGAVDRMMYSDMVDYLPDDILVKmDRASMAVGLEMRAPLL 536
                                               2223334445555555556667778888999************************************** PP

                                 TIGR01536 472 DkelvelalsippelklrdgkeKvlLreaaeellPeeileRkKeaf 517
                                               D ++vela++ p  l + +   K  Lr ++ + lPe+  + +K++f
  lcl|NCBI__GCF_000018545.1:YP_002823396.1 537 DYRFVELAWRAPRALCFAEAPGKPALRALLSRRLPEQFINLSKRGF 582
                                               ****************************************999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (653 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 8.58
//
[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