Alignments for a candidate for asnB in Sphingomonas koreensis DSMZ 15582

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Sphingomonas koreensis DSMZ 15582

Align Putative asparagine synthetase [glutamine-hydrolyzing]; EC 6.3.5.4 (characterized)
to candidate Ga0059261_4199 Ga0059261_4199 asparagine synthase (glutamine-hydrolyzing)

Query= SwissProt::P64248
         (652 letters)



>FitnessBrowser__Korea:Ga0059261_4199
          Length = 630

 Score =  290 bits (743), Expect = 1e-82
 Identities = 216/652 (33%), Positives = 319/652 (48%), Gaps = 58/652 (8%)

Query: 1   MCGLLAFVAAPAGAAGPEGADAASAIARASHLMRHRGPDESGTWHAVDGASGGVVFGFNR 60
           MCG+        G   P       A+A A   + HRGPD SG W A      G+  G  R
Sbjct: 1   MCGIAGLYYP--GVPKPVEPQRIKAMADA---LAHRGPDGSGAWTAP-----GIGLGHRR 50

Query: 61  LSIIDIAHSHQPLRWGPPEAPDRYVLVFNGEIYNYLELRDELRTQHGAVFATDGDGEAIL 120
           LSIID+A   QP+    PE     V+ +NGEIYN+LE+R EL  + GA F ++ D E +L
Sbjct: 51  LSIIDLAGGAQPM--ATPEGD--VVVSYNGEIYNFLEVRRELEAK-GAQFLSNSDTEVLL 105

Query: 121 AGYHHWGTEVLQRLRGMFAFALWDTVTRELFCARDPFGIKPL-FIATGAGGTAVASEKKC 179
            G+  WG+ +L +L GMFA AL+D  ++ L  ARD  G+KPL ++    G  A ASE K 
Sbjct: 106 HGWRAWGSAMLGKLNGMFAIALYDARSKSLMLARDRLGVKPLHYVELSDGAVAFASEIKG 165

Query: 180 LLDLVELVGFDTEIDHRALQHYTVLQYVPEPETLHRGVRRLESGCFARIRADQLAPVITR 239
           LL       F  + D  A++ +  L YVP+  ++  GV++L +G +  +   +  P  T 
Sbjct: 166 LL---AHPLFRRQPDFNAIEDFLGLGYVPDDASVLAGVKKLPAGHYLLLERGKPVPAPTE 222

Query: 240 YFVPRFAASPITNDNDQARYDEITAVLEDSVAKHMRADVTVGAFLSGGIDSTAIAALAIR 299
           ++   F  S  T  + +    E+   +  ++   M ADV +GAFLSGG+DS+A+ AL   
Sbjct: 223 WWDVDF--SKRTKGSARDLEAELIEHMRAAIQSRMIADVPLGAFLSGGVDSSAVVALMAE 280

Query: 300 HNPRLI-TFTTGFEREGFSEIDVAVASAEAIGARHIAKVVSADEFVAALPEIVWYLDEPV 358
            +   +   T GF+     E   A A AE     H  + V+AD+F A +  +V + DEP 
Sbjct: 281 ASRNAVKACTIGFDETDHDERVYARAVAERFCTEHRTRTVAADDF-ALIDALVHHFDEPF 339

Query: 359 ADPALVPLFFVAREARKHVKVVLSGEGADELFGGYTIYR-----------EPLSLR---- 403
           AD + +  + V   AR+ V V LSG+GADE   GY  YR            P + R    
Sbjct: 340 ADASALATYRVCELARETVTVALSGDGADEALAGYRRYRFHAAEERVRGLFPATARQGVF 399

Query: 404 --------PFDYLPKPLRRSMGKVSKPLPEGMRGKSLLHRGSLTLEERYYGNARSFSGAQ 455
                     D+ P+PLR     ++     G      +   +LT+    Y +A       
Sbjct: 400 GTLGRLYPKADWAPRPLRAKTTLLALAEDGGAAYAKAVGVTALTVRMGLYTDA------- 452

Query: 456 LREVLPGFRPDWTHTDVTAPVYAESAGWDPVARMQHIDLFTWLRGDILVKADKITMANSL 515
            R +L G R +  + +      A     D + R Q+ D   WL GDIL K D+ +MA SL
Sbjct: 453 ARALLGGHRAETRYVETMRNAPAR----DGLDRAQYADFKHWLPGDILTKMDRTSMAVSL 508

Query: 516 ELRVPFLDPEVFAVASRLPAGAKITRTTTKYALRRALEPIVPAHVLHRPKLGFPVPIRHW 575
           E R P LD      A+ LPA  +I     K+ +++ALEP +P  +L+RPK+GF  P+  W
Sbjct: 509 EAREPLLDYRFVEFAATLPASMRIRGGQGKWLMKKALEPWLPKDILYRPKMGFVTPVSAW 568

Query: 576 LRAGELLEWAYATVGSSQAGH-LVDIAAVYRMLDEHRCGSSDHSRRLWTMLI 626
            R     + A  +  +  AG    +  A+ R+ +EHR G ++H R LW +++
Sbjct: 569 FRTALADDAAALSRSAVLAGSGWFEPKAIARLAEEHRSGRAEHGRTLWQLMM 620


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: 1029
Number of extensions: 54
Number of successful extensions: 10
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: 630
Length adjustment: 38
Effective length of query: 614
Effective length of database: 592
Effective search space:   363488
Effective search space used:   363488
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 Ga0059261_4199 Ga0059261_4199 (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.30628.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.1e-145  471.5   0.0   2.5e-145  471.3   0.0    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_4199  Ga0059261_4199 asparagine syntha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_4199  Ga0059261_4199 asparagine synthase (glutamine-hydrolyzing)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  471.3   0.0  2.5e-145  2.5e-145       1     517 []       2     561 ..       2     561 .. 0.88

  Alignments for each domain:
  == domain 1  score: 471.3 bits;  conditional E-value: 2.5e-145
                                 TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsnek 69 
                                               Cgiag+         e + ik+m+++lahRGPD++g w      + +lghrRL+iidl +gaQP++  +
  lcl|FitnessBrowser__Korea:Ga0059261_4199   2 CGIAGLYYPGVPKPVEPQRIKAMADALAHRGPDGSGAWTA---PGIGLGHRRLSIIDLAGGAQPMATPE 67 
                                               9****9998777666899*********************9...7***********************99 PP

                                 TIGR01536  70 .evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelf 137
                                                 vv+ +nGEIYN+ e+r+ele+kG +F ++sDtEV+L+ +++wg +++ +L+GmFA+al+d++++ l+
  lcl|FitnessBrowser__Korea:Ga0059261_4199  68 gDVVVSYNGEIYNFLEVRRELEAKGAQFLSNSDTEVLLHGWRAWGSAMLGKLNGMFAIALYDARSKSLM 136
                                               999****************************************************************** PP

                                 TIGR01536 138 laRDrlGikPLYyase.qgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelep 205
                                               laRDrlG+kPL+y +  +g+++faSEiK+lla++ +++++d +a+ ++l+l +vp++ ++ ++vk+l++
  lcl|FitnessBrowser__Korea:Ga0059261_4199 137 LARDRLGVKPLHYVELsDGAVAFASEIKGLLAHPLFRRQPDFNAIEDFLGLGYVPDDASVLAGVKKLPA 205
                                               *************99889*************************************************** PP

                                 TIGR01536 206 akal.....dgeekleeywevekee.vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslv 268
                                               +++l     ++  +  e+w+v+ ++ +k s ++l +el e +++a+++r++advp+g++lSGG+DSs+v
  lcl|FitnessBrowser__Korea:Ga0059261_4199 206 GHYLllergKPVPAPTEWWDVDFSKrTKGSARDLEAELIEHMRAAIQSRMIADVPLGAFLSGGVDSSAV 274
                                               ****8876655556666*****988688999************************************** PP

                                 TIGR01536 269 aaiakkeaksevktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptai 337
                                               +a++++ ++++vk  +igf+ + d de  +ar+va+ + teh++ ++ ++++ + ++ ++++++ep+a+
  lcl|FitnessBrowser__Korea:Ga0059261_4199 275 VALMAEASRNAVKACTIGFD-ETDHDERVYARAVAERFCTEHRTRTVAADDF-ALIDALVHHFDEPFAD 341
                                               ********************.***************************9997.589************* PP

                                 TIGR01536 338 rasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeeale...................... 384
                                               +++  +y +++lare  v+V+LsG+GaDE ++GY ++r   aee+++                      
  lcl|FitnessBrowser__Korea:Ga0059261_4199 342 ASALATYRVCELARET-VTVALSGDGADEALAGYRRYRFHAAEERVRglfpatarqgvfgtlgrlypka 409
                                               ****************.********************************99998888888888887775 PP

                                 TIGR01536 385 ..........lpeaselaekkl...................llqaklakeselkellkakleeelke.. 422
                                                         +          +                   +   +  +    +  ++a l  +++e  
  lcl|FitnessBrowser__Korea:Ga0059261_4199 410 dwaprplrakT----------TllalaedggaayakavgvtA---LTVRMGLYTDAARALLGGHRAEtr 465
                                               55554444430..........144445555554444443321...222222222222222222222200 PP

                                 TIGR01536 423 keelkkelkeeseleellrldlelllsdllrak.DrvsmahslEvRvPflDkelvelalsippelklrd 490
                                                 e+ ++ +++  l++++++d++ +l+++++ k Dr+sma slE+R P+lD ++ve+a+++p+++++r 
  lcl|FitnessBrowser__Korea:Ga0059261_4199 466 YVETMRNAPARDGLDRAQYADFKHWLPGDILTKmDRTSMAVSLEAREPLLDYRFVEFAATLPASMRIRG 534
                                               23333344444899******************************************************* PP

                                 TIGR01536 491 gkeKvlLreaaeellPeeileRkKeaf 517
                                               g+ K+l+++a+e  lP++il+R+K++f
  lcl|FitnessBrowser__Korea:Ga0059261_4199 535 GQGKWLMKKALEPWLPKDILYRPKMGF 561
                                               *************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (630 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: 10.89
//
[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