Alignments for a candidate for asnB in Sinorhizobium meliloti 1021

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Sinorhizobium meliloti 1021

Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate SM_b20652 SM_b20652 asparagine synthetase

Query= CharProtDB::CH_005185
         (632 letters)



>FitnessBrowser__Smeli:SM_b20652
          Length = 645

 Score =  272 bits (695), Expect = 4e-77
 Identities = 192/600 (32%), Positives = 303/600 (50%), Gaps = 35/600 (5%)

Query: 1   MCGFVGVFNKHPLAQTADQEELIKQMNQMIVHRGPDSDGYFHDEHVGFGFRRLSIIDVEN 60
           MCGF G      L    D + L+++M   I HRGPD  G F     G G  RLSI+ + +
Sbjct: 1   MCGFGGY-----LGSIRDGKPLLERMTAAIGHRGPDERGIFTAPGAGLGHVRLSIVGLGD 55

Query: 61  GGQPLSYEDETYWIIFNGEIYNYIELREELEAKGYTFNTDSDTEVLLATYRHYKEEAASK 120
           G QP+S       I FNGEI+NY+ELR+EL A+G  F T SDTEV+L  Y    E+  S 
Sbjct: 56  GQQPMSNPSGELTIAFNGEIFNYVELRDELRARGRQFRTSSDTEVILHLYEEMGEDCLSL 115

Query: 121 LRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTINDQVYFASERKSLM-VAQNDIEIDKE 179
           L G FAF IW+     +  ARD  G++PL++T     +YFASE K+L+ V     EID  
Sbjct: 116 LNGDFAFAIWDARRRRMMLARDRMGVRPLFHTLKGGTLYFASEVKALLEVPGVSAEIDPI 175

Query: 180 ALQQYMSFQFVPEPSTLDAHVKKVEPGSQFTIRPDGDITFKTYFKANF-----KPVQTEE 234
           AL Q  +      P T    + ++EPG       +G  T + Y++ ++     +P   EE
Sbjct: 176 ALDQIFTLWAPIAPRTPFRDIHELEPGHLMIADQNGTTT-RPYWQLDYPDRDERPAYAEE 234

Query: 235 DKLVKEVRDAIYDSVNVHMRSDVPVGSFLSGGIDSSFIVSVAKEF-HPSLKTFSVGFEQQ 293
            +  +E+R  + D+  + MR+DVPVG++LSGG+DSS I ++A       L+TFSV F+  
Sbjct: 235 SRAAEELRALLTDATRIRMRADVPVGAYLSGGLDSSIISALAAGMTSQGLRTFSVTFDSA 294

Query: 294 GFSEVDVAKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADPAAIPLYFVAKEAK 353
              E    +E AAALG E+ +      +   + P ++   + P+   A  PLY ++   +
Sbjct: 295 EHDESAFQEEMAAALGTEHRAVACRAGDIARDFPDVIRFTEKPIIRTAPAPLYKLSGLVR 354

Query: 354 KH-VTVALSGEGADELFGGYNIYREP-----LSLKPFERI-PSGLKKMLLHVAAVMPEGM 406
           +  + V L+GEGADE+F GY+I++E         +P  RI P   +K+  ++  +  +  
Sbjct: 355 EAGLKVVLTGEGADEVFAGYDIFKEARVRRFCGRQPGSRIRPHLFRKLYPYLPGLQQQSA 414

Query: 407 R--------GKSLLERGCTPLQDRYIGNA--KIFEESVKKQLLKHYNPNLSYRDVTKTYF 456
                    G   L+      + R  G A  K+F  S  +  L  Y+   +  ++     
Sbjct: 415 EYLAAFFGAGDVALDDPLFSHRPRLKGTAATKMFFSSDLRAELTGYD---AAEELVSRLP 471

Query: 457 TESSSYSDINKMQYVDIHTWMRGDILL-KADKMTMANSLELRVPFLDKVVFDVASKIPDE 515
                +  +++ QY++    + G IL  + D+M MA+ +E R PFLD  + + A+K+P E
Sbjct: 472 AAFGRWHPLHQAQYLESRFLLPGYILSSQGDRMAMAHGIEGRFPFLDHRLVEFAAKLPPE 531

Query: 516 LKTKNGTTKYLLRKAAEGIVPEHVLNRKKLGFPVPIRHWLKNEMN-EWVRNIIQESQTDA 574
           +K +    K++LR+A + ++P  +  R K  +  P  H        ++VR+ + E    A
Sbjct: 532 MKLRGLVEKHILREATKDLLPPAIGRRTKQPYRAPDSHSFSGAGELDYVRSAMSEDAVAA 591


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: 888
Number of extensions: 38
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 632
Length of database: 645
Length adjustment: 38
Effective length of query: 594
Effective length of database: 607
Effective search space:   360558
Effective search space used:   360558
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: 54 (25.4 bits)

Align candidate SM_b20652 SM_b20652 (asparagine synthetase)
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.15843.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-157  511.7   0.0   1.7e-157  511.5   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SM_b20652  SM_b20652 asparagine synthetase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SM_b20652  SM_b20652 asparagine synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  511.5   0.0  1.7e-157  1.7e-157       1     517 []       2     563 ..       2     563 .. 0.90

  Alignments for each domain:
  == domain 1  score: 511.5 bits;  conditional E-value: 1.7e-157
                            TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsnek.evvi 73 
                                          Cg+ g + +    ++ +  +++m+ ++ hRGPD++g++      +a+lgh+RL+i+ l +g+QP+sn + e +i
  lcl|FitnessBrowser__Smeli:SM_b20652   2 CGFGGYLGSI---RDGKPLLERMTAAIGHRGPDERGIFTA---PGAGLGHVRLSIVGLGDGQQPMSNPSgELTI 69 
                                          6777776663...3456799******************99...7****************************** PP

                            TIGR01536  74 vfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlGikP 147
                                           fnGEI+N+ eLr+el+++G +F+t sDtEViL++yee+ge++++ L+G+FAfa+wd+++++++laRDr+G++P
  lcl|FitnessBrowser__Smeli:SM_b20652  70 AFNGEIFNYVELRDELRARGRQFRTSSDTEVILHLYEEMGEDCLSLLNGDFAFAIWDARRRRMMLARDRMGVRP 143
                                          ************************************************************************** PP

                            TIGR01536 148 LYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakal...dgeekleey 218
                                          L+++ ++g+l+faSE+Kall+++ + ae+d  al +++tl+    ++t f++++elep++ +   ++ ++ + y
  lcl|FitnessBrowser__Smeli:SM_b20652 144 LFHTLKGGTLYFASEVKALLEVPGVSAEIDPIALDQIFTLWAPIAPRTPFRDIHELEPGHLMiadQNGTTTRPY 217
                                          *****************************************999*****************999655555566* PP

                            TIGR01536 219 wevekee.....vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeaksevktFsigf 287
                                          w+++++        ++e+++ eelr ll+da++ r++advpvg++lSGGlDSs+++a+a+    + ++tFs+ f
  lcl|FitnessBrowser__Smeli:SM_b20652 218 WQLDYPDrderpAYAEESRAAEELRALLTDATRIRMRADVPVGAYLSGGLDSSIISALAAGMTSQGLRTFSVTF 291
                                          ****9998888777889999****************************************************** PP

                            TIGR01536 288 edskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasiplyllsklarekgvkVvLsG 361
                                          + s++ des++++++a++lgteh+ v   + +++ ++++vi+ +e+p+  +a +ply ls l+re g+kVvL+G
  lcl|FitnessBrowser__Smeli:SM_b20652 292 D-SAEHDESAFQEEMAAALGTEHRAVACRAGDIARDFPDVIRFTEKPIIRTAPAPLYKLSGLVREAGLKVVLTG 364
                                          *.************************************************************************ PP

                            TIGR01536 362 eGaDElfgGYeyfreakaeeale..................lpeaselaekkl...................ll 398
                                          eGaDE+f+GY++f+ea +++ +                   l     l++++                     +
  lcl|FitnessBrowser__Smeli:SM_b20652 365 EGADEVFAGYDIFKEARVRRFCGrqpgsrirphlfrklypyL---PGLQQQSAeylaaffgagdvalddplfSH 435
                                          ****************99999998999999888888885552...33333333455667788888888888755 PP

                            TIGR01536 399 qaklakeselkellkakleeelkekeelkkelkee.......seleellrldlelllsdllrak..Drvsmahs 463
                                          + +l+ + ++k +++ +l++el+  ++ ++ +++        + l+++++l+   ll+++++ +  Dr++mah+
  lcl|FitnessBrowser__Smeli:SM_b20652 436 RPRLKGTAATKMFFSSDLRAELTGYDAAEELVSRLpaafgrwHPLHQAQYLESRFLLPGYILSSqgDRMAMAHG 509
                                          555555666666666666666666655555555555566666*******************9999********* PP

                            TIGR01536 464 lEvRvPflDkelvelalsippelklrdgkeKvlLreaaeellPeeileRkKeaf 517
                                          +E R+PflD++lve+a+++ppe+klr   eK++Lrea ++llP +i  R K+++
  lcl|FitnessBrowser__Smeli:SM_b20652 510 IEGRFPFLDHRLVEFAAKLPPEMKLRGLVEKHILREATKDLLPPAIGRRTKQPY 563
                                          ***************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (645 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: 00:00:00.03
# Mc/sec: 10.64
//
[ok]

This GapMind analysis is from Apr 09 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