Alignments for a candidate for asnB in Desulfovibrio vulgaris Hildenborough

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Desulfovibrio vulgaris Hildenborough

Align Putative asparagine synthetase [glutamine-hydrolyzing]; EC 6.3.5.4 (characterized)
to candidate 208527 DVU3014 asparagine synthetase, glutamine-hydrolyzing

Query= SwissProt::P64248
         (652 letters)



>MicrobesOnline__882:208527
          Length = 697

 Score =  303 bits (776), Expect = 2e-86
 Identities = 227/660 (34%), Positives = 316/660 (47%), Gaps = 42/660 (6%)

Query: 1   MCGLLAFVAAPAGAAGPEGADAASAIARASHLMRHRGPDESGTWHAVDGA-SGGVVFGFN 59
           MCG+       AG   P    A++ +A  +  + HRGPD  G +    GA S  V  G  
Sbjct: 1   MCGI-------AGIVSPGAPVASATLAAMTESLAHRGPDACGLFIRPSGAGSPHVGLGHR 53

Query: 60  RLSIIDIAHSH-QPLRWGPPEAPDRYVLVFNGEIYNYLELRDELRTQHGAVFATDGDGEA 118
           RLSI+D++ +  QP++         + LVFNGEIYNY +LR +L    G +F +  D EA
Sbjct: 54  RLSILDLSDAGAQPMQ----SEDGAFTLVFNGEIYNYPDLRRDLEAA-GHIFRSTSDTEA 108

Query: 119 ILAGYHHWGTEVLQRLRGMFAFALWDTVTRELFCARDPFGIKPLFIATGAGGTAV-ASEK 177
           IL GY  WG  V+ RL+GMFAFALWD   R L  ARD FG KPL  A    GT + ASE 
Sbjct: 109 ILRGYMAWGEGVVARLKGMFAFALWDERKRSLLLARDRFGKKPLHYAVTRQGTLLFASEP 168

Query: 178 KCLLDLVELVGFDTEIDHRALQHYTVLQYVPEPETLHRGVRRLESGCFARIRADQLAPVI 237
           K LL   E   F  E D  +L H+    YVP P +++ G  +L        R  +L   +
Sbjct: 169 KALLAHPE---FRPEPDAASLLHFLRYDYVPAPRSIYAGAAKLPPSHLMVWRDGRLE--V 223

Query: 238 TRYFVPRFAASPITNDNDQARYDE---ITAVLEDSVAKHMRADVTVGAFLSGGIDSTAIA 294
            RY     A S  T D      +    + A+L+ +V + + +DV +G FLSGG+DS+ + 
Sbjct: 224 RRY--ASLAFSGATGDRGVPLREAEAAVDALLDAAVQRRLASDVPLGVFLSGGLDSSTVL 281

Query: 295 ALAIRHNPR--LITFTTGFEREGFSEIDVAVASAEAIGARHIAKVVSADEFVAALPEIVW 352
           A   RH P   + TF  GF+   + E   A A A   G+ H    + A   +  L  +  
Sbjct: 282 AYMTRHIPAHDIRTFAIGFDEASYDESAHAEAMARHAGSHHTMMRLPAARMLDLLDMVWT 341

Query: 353 YLDEPVADPALVPLFFVAREARKHVKVVLSGEGADELFGGYTIYREPLSLRPFDYLPKPL 412
             DEP+AD +++P   + R AR+H+ V L G+G DELF GY      L  R  D+LP   
Sbjct: 342 TQDEPMADASIIPTLLLCRFAREHITVALGGDGGDELFAGYDPVLADLPARCLDWLPPAA 401

Query: 413 RRSMGKVSKPLPEGMRGKSLLHR--------GSLTLEERYYGNARSFSGAQLREVL-PGF 463
            R +  ++  LP G    SL  +        G+  +  R+     +F     R +L P  
Sbjct: 402 LRLLQGIALRLPTGDANMSLGFKVQRFLSGLGAREVAARHQTWLGAFDDEGARAMLHPDL 461

Query: 464 RP---DWTHTDVTAPVYAESAGWDPVARMQHIDLFTWLRGDILVKADKITMANSLELRVP 520
           R    D +  D    +  E         M H     ++ G IL K D  +MA SLE+R P
Sbjct: 462 RAATRDVSPLDALDMLREECRDASRFDAMLHFYQRFYMCGSILTKVDSASMAVSLEVRSP 521

Query: 521 FLDPEVFAVASRLPAGAKITRTTTKYALRRALEPIVPAHVLHRPKLGFPVPIRHWLRAGE 580
           FLD ++    +RLP   K+   T K  LRR +   +P  +L RPK GF +P+  W R  E
Sbjct: 522 FLDQDLADYVNRLPREHKLRGLTRKVLLRRLMRSRMPDALLKRPKKGFGLPLARWFR-HE 580

Query: 581 L--LEWAYATVGSSQAGHLVDIAAVYRMLDEHRCGSSDHSRRLWTMLIFMLWHAIFVEHS 638
           L  L  A    G    G L+D   V RM+ +H  G  DH + +W+ L    W   ++ HS
Sbjct: 581 LRPLVTAMLDPGRVAQGGLLDPVTVERMVRDHLSGRRDHRKEIWSALCVEAWRERYLHHS 640


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: 1192
Number of extensions: 71
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: 652
Length of database: 697
Length adjustment: 39
Effective length of query: 613
Effective length of database: 658
Effective search space:   403354
Effective search space used:   403354
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 208527 DVU3014 (asparagine synthetase, 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.477.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-142  461.7   0.0   2.5e-142  461.4   0.0    1.1  1  lcl|MicrobesOnline__882:208527  DVU3014 asparagine synthetase, g


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:208527  DVU3014 asparagine synthetase, glutamine-hydrolyzing
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  461.4   0.0  2.5e-142  2.5e-142       1     517 []       2     569 ..       2     569 .. 0.88

  Alignments for each domain:
  == domain 1  score: 461.4 bits;  conditional E-value: 2.5e-142
                       TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkd...ekeenailghrRLaiidlseg.aQPlsnek.evviv 74 
                                     Cgiagiv   a +++  +++++m+e lahRGPDa g+++    + + +++lghrRL+i dls++ aQP+++e+ + ++v
  lcl|MicrobesOnline__882:208527   2 CGIAGIVSPGAPVAS--ATLAAMTESLAHRGPDACGLFIRpsgAGSPHVGLGHRRLSILDLSDAgAQPMQSEDgAFTLV 78 
                                     ********9776554..79********************965435679**************999*********99*** PP

                       TIGR01536  75 fnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlGikPLYyase 153
                                     fnGEIYN+ +Lr++le++G+ F+++sDtE iL+ y +wge +v+rL+GmFAfalwde+k+ l+laRDr+G+kPL+ya +
  lcl|MicrobesOnline__882:208527  79 FNGEIYNYPDLRRDLEAAGHIFRSTSDTEAILRGYMAWGEGVVARLKGMFAFALWDERKRSLLLARDRFGKKPLHYAVT 157
                                     *****************************************************************************99 PP

                       TIGR01536 154 .qgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakal...dgeekleeywevekee... 225
                                      qg+llfaSE Kalla++e+++e+d++ l ++l + +vp +++++++  +l+p++ +   dg  ++++y +++ +    
  lcl|MicrobesOnline__882:208527 158 rQGTLLFASEPKALLAHPEFRPEPDAASLLHFLRYDYVPAPRSIYAGAAKLPPSHLMvwrDGRLEVRRYASLAFSGatg 236
                                     9*******************************************************99998888999999999988555 PP

                       TIGR01536 226 .vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeak.sevktFsigfedskdldeskaarkv 302
                                      +   ++e+ + ++ ll +av++rl +dvp+gv+lSGGlDSs+v a + ++++ ++++tF+igf+ ++++des++a+++
  lcl|MicrobesOnline__882:208527 237 dRGVPLREAEAAVDALLDAAVQRRLASDVPLGVFLSGGLDSSTVLAYMTRHIPaHDIRTFAIGFD-EASYDESAHAEAM 314
                                     555567899999***************************************99999*********.************* PP

                       TIGR01536 303 adelgtehkevliseeevlkeleevilaleeptairasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaee 381
                                     a++ g++h+ + + ++ +l+ l+ v  +++ep+a++++ip++ll++ are+ ++V+L+G+G+DElf+GY+       ++
  lcl|MicrobesOnline__882:208527 315 ARHAGSHHTMMRLPAARMLDLLDMVWTTQDEPMADASIIPTLLLCRFAREH-ITVALGGDGGDELFAGYDPVLADLPAR 392
                                     ***************************************************.**********************99999 PP

                       TIGR01536 382 ale...............................lpeaselaekkl...................llqaklakeselke 410
                                     +l                                           +                   + ++  ++  +   
  lcl|MicrobesOnline__882:208527 393 CLDwlppaalrllqgialrlptgdanmslgfkvqR----------FlsglgarevaarhqtwlgaFDDEGARAMLHPDL 461
                                     99999999988888887776665544444433330..........2444444444443333444322222222222222 PP

                       TIGR01536 411 llkakleeelkekeelkkelkeeseleellrldlelllsdllrak.DrvsmahslEvRvPflDkelvelalsippelkl 488
                                      + ++  + l   + l +e   +s+++++l+     ++ + ++ k D +sma slEvR PflD++l++++ ++p e+kl
  lcl|MicrobesOnline__882:208527 462 RAATRDVSPLDALDMLREECRDASRFDAMLHFYQRFYMCGSILTKvDSASMAVSLEVRSPFLDQDLADYVNRLPREHKL 540
                                     33333333444455555555555******************************************************** PP

                       TIGR01536 489 rdgkeKvlLreaaeellPeeileRkKeaf 517
                                     r  ++KvlLr+++++ +P+++l+R+K++f
  lcl|MicrobesOnline__882:208527 541 RGLTRKVLLRRLMRSRMPDALLKRPKKGF 569
                                     **************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (697 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: 11.22
//
[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