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 asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate Ga0059261_4199 Ga0059261_4199 asparagine synthase (glutamine-hydrolyzing)

Query= CharProtDB::CH_005185
         (632 letters)



>FitnessBrowser__Korea:Ga0059261_4199
          Length = 630

 Score =  285 bits (730), Expect = 3e-81
 Identities = 193/631 (30%), Positives = 326/631 (51%), Gaps = 38/631 (6%)

Query: 1   MCGFVGVFNKHPLAQTADQEELIKQMNQMIVHRGPDSDGYFHDEHVGFGFRRLSIIDVEN 60
           MCG  G++  +P      + + IK M   + HRGPD  G +    +G G RRLSIID+  
Sbjct: 1   MCGIAGLY--YPGVPKPVEPQRIKAMADALAHRGPDGSGAWTAPGIGLGHRRLSIIDLAG 58

Query: 61  GGQPLSYEDETYWIIFNGEIYNYIELREELEAKGYTFNTDSDTEVLLATYRHYKEEAASK 120
           G QP++  +    + +NGEIYN++E+R ELEAKG  F ++SDTEVLL  +R +      K
Sbjct: 59  GAQPMATPEGDVVVSYNGEIYNFLEVRRELEAKGAQFLSNSDTEVLLHGWRAWGSAMLGK 118

Query: 121 LRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTIND-QVYFASERKSLMV-AQNDIEIDK 178
           L GMFA  +++     L  ARD  G+KPL+Y  ++D  V FASE K L+       + D 
Sbjct: 119 LNGMFAIALYDARSKSLMLARDRLGVKPLHYVELSDGAVAFASEIKGLLAHPLFRRQPDF 178

Query: 179 EALQQYMSFQFVPEPSTLDAHVKKVEPGSQFTIRPDG----------DITFKTYFKANFK 228
            A++ ++   +VP+ +++ A VKK+ P   + +   G          D+ F    K + +
Sbjct: 179 NAIEDFLGLGYVPDDASVLAGVKKL-PAGHYLLLERGKPVPAPTEWWDVDFSKRTKGSAR 237

Query: 229 PVQTEEDKLVKEVRDAIYDSVNVHMRSDVPVGSFLSGGIDSSFIVS-VAKEFHPSLKTFS 287
            ++ E   L++ +R AI       M +DVP+G+FLSGG+DSS +V+ +A+    ++K  +
Sbjct: 238 DLEAE---LIEHMRAAIQS----RMIADVPLGAFLSGGVDSSAVVALMAEASRNAVKACT 290

Query: 288 VGFEQQGFSEVDVAKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADPAAIPLYF 347
           +GF++    E   A+  A     E+ ++ ++ +++   +  +V HFD+P AD +A+  Y 
Sbjct: 291 IGFDETDHDERVYARAVAERFCTEHRTRTVAADDFA-LIDALVHHFDEPFADASALATYR 349

Query: 348 VAKEAKKHVTVALSGEGADELFGGYNIYREPLSLKPFERI-PS-------GLKKMLLHVA 399
           V + A++ VTVALSG+GADE   GY  YR   + +    + P+       G    L   A
Sbjct: 350 VCELARETVTVALSGDGADEALAGYRRYRFHAAEERVRGLFPATARQGVFGTLGRLYPKA 409

Query: 400 AVMPEGMRGKSLLERGCTPLQDRYIGNAKIFEESVKKQLLKHYNPNLSYRDVTKTYFTE- 458
              P  +R K+ L          Y     +   +V+  L       L      +T + E 
Sbjct: 410 DWAPRPLRAKTTLLALAEDGGAAYAKAVGVTALTVRMGLYTDAARALLGGHRAETRYVET 469

Query: 459 ---SSSYSDINKMQYVDIHTWMRGDILLKADKMTMANSLELRVPFLDKVVFDVASKIPDE 515
              + +   +++ QY D   W+ GDIL K D+ +MA SLE R P LD    + A+ +P  
Sbjct: 470 MRNAPARDGLDRAQYADFKHWLPGDILTKMDRTSMAVSLEAREPLLDYRFVEFAATLPAS 529

Query: 516 LKTKNGTTKYLLRKAAEGIVPEHVLNRKKLGFPVPIRHWLKNEMNEWVRNIIQES--QTD 573
           ++ + G  K+L++KA E  +P+ +L R K+GF  P+  W +  + +    + + +     
Sbjct: 530 MRIRGGQGKWLMKKALEPWLPKDILYRPKMGFVTPVSAWFRTALADDAAALSRSAVLAGS 589

Query: 574 AYIHKDYVLQLLEDHCADKADNSRKIWTVLI 604
            +     + +L E+H + +A++ R +W +++
Sbjct: 590 GWFEPKAIARLAEEHRSGRAEHGRTLWQLMM 620


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: 838
Number of extensions: 42
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: 2
Length of query: 632
Length of database: 630
Length adjustment: 38
Effective length of query: 594
Effective length of database: 592
Effective search space:   351648
Effective search space used:   351648
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 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.3534776.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  FitnessBrowser__Korea:Ga0059261_4199  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Korea:Ga0059261_4199  
   #    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.evv 72 
                                           Cgiag+         e + ik+m+++lahRGPD++g w      + +lghrRL+iidl +gaQP++  +  vv
  FitnessBrowser__Korea:Ga0059261_4199   2 CGIAGLYYPGVPKPVEPQRIKAMADALAHRGPDGSGAWTA---PGIGLGHRRLSIIDLAGGAQPMATPEgDVV 71 
                                           9****9998777666899*********************9...7***********************99999* PP

                             TIGR01536  73 ivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlGi 145
                                           + +nGEIYN+ e+r+ele+kG +F ++sDtEV+L+ +++wg +++ +L+GmFA+al+d++++ l+laRDrlG+
  FitnessBrowser__Korea:Ga0059261_4199  72 VSYNGEIYNFLEVRRELEAKGAQFLSNSDTEVLLHGWRAWGSAMLGKLNGMFAIALYDARSKSLMLARDRLGV 144
                                           ************************************************************************* PP

                             TIGR01536 146 kPLYyase.qgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakal.....dge 212
                                           kPL+y +  +g+++faSEiK+lla++ +++++d +a+ ++l+l +vp++ ++ ++vk+l+++++l     ++ 
  FitnessBrowser__Korea:Ga0059261_4199 145 KPLHYVELsDGAVAFASEIKGLLAHPLFRRQPDFNAIEDFLGLGYVPDDASVLAGVKKLPAGHYLllergKPV 217
                                           *****99889*******************************************************88766555 PP

                             TIGR01536 213 ekleeywevekee.vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeaksevktFs 284
                                            +  e+w+v+ ++ +k s ++l +el e +++a+++r++advp+g++lSGG+DSs+v+a++++ ++++vk  +
  FitnessBrowser__Korea:Ga0059261_4199 218 PAPTEWWDVDFSKrTKGSARDLEAELIEHMRAAIQSRMIADVPLGAFLSGGVDSSAVVALMAEASRNAVKACT 290
                                           56666*****988688999****************************************************** PP

                             TIGR01536 285 igfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasiplyllsklarekgvkV 357
                                           igf+ + d de  +ar+va+ + teh++ ++ ++++ + ++ ++++++ep+a++++  +y +++lare  v+V
  FitnessBrowser__Korea:Ga0059261_4199 291 IGFD-ETDHDERVYARAVAERFCTEHRTRTVAADDF-ALIDALVHHFDEPFADASALATYRVCELARET-VTV 360
                                           ****.***************************9997.589*****************************.*** PP

                             TIGR01536 358 vLsGeGaDElfgGYeyfreakaeeale................................lpeaselaekkl.. 396
                                           +LsG+GaDE ++GY ++r   aee+++                                +          +  
  FitnessBrowser__Korea:Ga0059261_4199 361 ALSGDGADEALAGYRRYRFHAAEERVRglfpatarqgvfgtlgrlypkadwaprplrakT----------Tll 423
                                           *****************************9999888888888888777555554444430..........144 PP

                             TIGR01536 397 .................llqaklakeselkellkakleeelke..keelkkelkeeseleellrldlelllsd 450
                                                            +   +  +    +  ++a l  +++e    e+ ++ +++  l++++++d++ +l++
  FitnessBrowser__Korea:Ga0059261_4199 424 alaedggaayakavgvtA---LTVRMGLYTDAARALLGGHRAEtrYVETMRNAPARDGLDRAQYADFKHWLPG 493
                                           445555554444443321...22222222222222222222220023333344444899************** PP

                             TIGR01536 451 llrak.DrvsmahslEvRvPflDkelvelalsippelklrdgkeKvlLreaaeellPeeileRkKeaf 517
                                           +++ k Dr+sma slE+R P+lD ++ve+a+++p+++++r g+ K+l+++a+e  lP++il+R+K++f
  FitnessBrowser__Korea:Ga0059261_4199 494 DILTKmDRTSMAVSLEAREPLLDYRFVEFAATLPASMRIRGGQGKWLMKKALEPWLPKDILYRPKMGF 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 18.68
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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