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_3119 Ga0059261_3119 asparagine synthase (glutamine-hydrolyzing)

Query= SwissProt::P64248
         (652 letters)



>FitnessBrowser__Korea:Ga0059261_3119
          Length = 616

 Score =  303 bits (777), Expect = 1e-86
 Identities = 220/640 (34%), Positives = 318/640 (49%), Gaps = 34/640 (5%)

Query: 1   MCGLLAFVAAPAGAAGPEGADAASAIARASHLMRHRGPDESGTWHAVDGASGGVVFGFNR 60
           MCG+       AG A       +  +  A   + HRGPD++G W + DG  G       R
Sbjct: 1   MCGI-------AGVASRHELPRSGWLGDAVGALHHRGPDDTGQWWSPDGRVG---LAQAR 50

Query: 61  LSIIDIAHS-HQPLRWGPPEAPDRYVLVFNGEIYNYLELRDELRTQHGAVFATDGDGEAI 119
           L+IID++   HQP+        DR  +VFNGEIYN+ +LR EL    G VF +  D E +
Sbjct: 51  LAIIDLSPGGHQPMH----READRLSVVFNGEIYNFRDLRAELEGL-GHVFRSHSDTEVL 105

Query: 120 LAGYHHWGTEVLQRLRGMFAFALWDTVTRELFCARDPFGIKPLFIATGAGGTAVASEKKC 179
           LA Y  WG   L RL GMFAFA++D    +++ ARD  G KPLF     G    ASE K 
Sbjct: 106 LAAYAQWGIGCLTRLNGMFAFAIFDARANKVYFARDRAGEKPLFYHAANGTIHFASELKT 165

Query: 180 LLDLVELVGFDTEIDHRALQHYTVLQYVPEPETLHRGVRRLESGCFARIRADQLAPVITR 239
           LL    L      ID  AL  Y +  YVP    +  G R+L  G    +     A  + R
Sbjct: 166 LLADPTL---PRVIDPAALDGYLLTGYVPGDGCILAGYRKLPPGHAMELDLSSGAHRVWR 222

Query: 240 YF-VPRFAASPITNDNDQARYDEITAVLEDSVAKHMRADVTVGAFLSGGIDSTAIAALAI 298
           Y+ +P +A      D+D     E+ A+LED+V + + ADV VG  LSGG+DS+ I A+A+
Sbjct: 223 YWNLPDYAP---VEDDDAGLLGELEALLEDAVGRQLVADVPVGVLLSGGVDSSLITAMAV 279

Query: 299 RHNPRLITFTTGFEREG-FSEIDVAVASAEAIGARHIAKVVSADEFVAALPEIVWYLDEP 357
           R+  ++ TFT GF   G  +EI+ A   A+  G   + ++++       LP +    DEP
Sbjct: 280 RNAAKVRTFTIGFAGAGPLNEIEHARLIADHFGTEQV-ELMAEPTVAELLPRLAAQFDEP 338

Query: 358 VADPALVPLFFVAREARKHVKVVLSGEGADELFGGYTIYREPLSLR-PFDYLPKPLRRSM 416
           +AD ++ P F V+   R+H  V L G+G DELFGGY  Y + L+LR     +P PLR   
Sbjct: 339 MADSSMFPTFMVSELVRQHCTVALGGDGGDELFGGYGHYSQLLALRAKVGAVPGPLRSLA 398

Query: 417 GKVSKP-LPEGMRGKSLLHRGSLTLEERYYGNARSFSGAQLREVLPGFRPDWTHTDVTAP 475
            + ++  LP G RG++ L    +         +  F  A  R++L G  P     D  + 
Sbjct: 399 ARTAETLLPLGFRGRNWLKGLDVDFRHGLPLPSGFFDAASRRKLLGGAHPITAEADYRSR 458

Query: 476 VYAESAGWDPVARMQHIDLFTWLRGDILVKADKITMANSLELRVPFLDPEVFAVA-SRLP 534
           + A     D + R    D  T+L  DILVK D+ +M  SLE+R PFLD  +   A  ++P
Sbjct: 459 IPAMD---DLLQRATRTDFGTYLSEDILVKVDRTSMLTSLEVRAPFLDHRLIEFAFGKVP 515

Query: 535 AGAKITRTTTKYALRRALEPIVPAHVLHRPKLGFPVPIRHWLRAGELLEWAYATVGSSQA 594
           +  K T +  K  L++    ++P     + K GF +P+  WL+AG   E  ++ +  +  
Sbjct: 516 SRLKATASDKKILLKQLAARVLPPQFDRQRKQGFSIPLADWLKAGPFREMFWSVL--TDC 573

Query: 595 GHLVDIAAVYRMLDEHRCGSSDHSRRLWTMLIFMLWHAIF 634
             L D  AV  +LD    G S +  RL+ +  F LW   +
Sbjct: 574 DCLFDRRAVQALLDGQDAGRS-NGDRLFALAQFELWRRAY 612


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: 995
Number of extensions: 41
Number of successful extensions: 9
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: 616
Length adjustment: 38
Effective length of query: 614
Effective length of database: 578
Effective search space:   354892
Effective search space used:   354892
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_3119 Ga0059261_3119 (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.3371037.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.1e-137  446.0   0.0   1.6e-137  445.6   0.0    1.2  1  FitnessBrowser__Korea:Ga0059261_3119  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Korea:Ga0059261_3119  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  445.6   0.0  1.6e-137  1.6e-137       1     517 []       2     549 ..       2     549 .. 0.89

  Alignments for each domain:
  == domain 1  score: 445.6 bits;  conditional E-value: 1.6e-137
                             TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsnek.ev 71 
                                           Cgiag+  +++  ++    +   + +l+hRGPD++g w + ++ +++l+++RLaiidls g +QP++ e+ + 
  FitnessBrowser__Korea:Ga0059261_3119   2 CGIAGVASRHELPRS--GWLGDAVGALHHRGPDDTGQWWS-PDGRVGLAQARLAIIDLSPGgHQPMHREAdRL 71 
                                           ******999886555..67888899***************.9*****************999********9** PP

                             TIGR01536  72 vivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlG 144
                                            +vfnGEIYN+++Lr+ele  G+ F+++sDtEV+Laay +wg  ++ rL+GmFAfa++d+++++++ aRDr G
  FitnessBrowser__Korea:Ga0059261_3119  72 SVVFNGEIYNFRDLRAELEGLGHVFRSHSDTEVLLAAYAQWGIGCLTRLNGMFAFAIFDARANKVYFARDRAG 144
                                           ************************************************************************* PP

                             TIGR01536 145 ikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakal.....dge 212
                                            kPL+y   +g+++faSE+K lla ++ ++ +d +al  +l   +vp + ++ ++ ++l+p++a+     +g+
  FitnessBrowser__Korea:Ga0059261_3119 145 EKPLFYHAANGTIHFASELKTLLADPTLPRVIDPAALDGYLLTGYVPGDGCILAGYRKLPPGHAMeldlsSGA 217
                                           *****************************************************************99999899 PP

                             TIGR01536 213 ekleeywevekee.vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeaksevktFs 284
                                           +++++yw++ + + v++++  l  el+ lledav ++lvadvpvgvllSGG+DSsl++a+a + a+ +v+tF+
  FitnessBrowser__Korea:Ga0059261_3119 218 HRVWRYWNLPDYApVEDDDAGLLGELEALLEDAVGRQLVADVPVGVLLSGGVDSSLITAMAVRNAA-KVRTFT 289
                                           99999***9887768999999*******************************************99.8***** PP

                             TIGR01536 285 igfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasiplyllsklarekgvkV 357
                                           igf++   l+e ++ar +ad++gte  e+ + e +v++ l+++  +++ep+a+++++p++++s+l+r++ ++V
  FitnessBrowser__Korea:Ga0059261_3119 290 IGFAGAGPLNEIEHARLIADHFGTEQVEL-MAEPTVAELLPRLAAQFDEPMADSSMFPTFMVSELVRQH-CTV 360
                                           ************************98775.67789999*******************************.*** PP

                             TIGR01536 358 vLsGeGaDElfgGYeyfreakaeeale..............lpeaselaekkl.................... 396
                                           +L+G+G+DElfgGY  + +  a +a                           +                    
  FitnessBrowser__Korea:Ga0059261_3119 361 ALGGDGGDELFGGYGHYSQLLALRAKVgavpgplrslaartA----------Etllplgfrgrnwlkgldvdf 423
                                           *******************98877665676666555433330..........133455555555566667776 PP

                             TIGR01536 397 ....llqaklakeselkellkakleeelkekeelkkelkeeseleellrldlelllsdllrak.Drvsmahsl 464
                                                l + ++++ + ++ll    +  ++e +  ++  + +  l++++r d+ ++ls+++++k Dr+sm  sl
  FitnessBrowser__Korea:Ga0059261_3119 424 rhglPLPSGFFDAASRRKLLG-GAHPITAEADYRSRIPAMDDLLQRATRTDFGTYLSEDILVKvDRTSMLTSL 495
                                           666644455555555555554.3333344444444444555999***************************** PP

                             TIGR01536 465 EvRvPflDkelvelal.sippelklrdgkeKvlLreaaeellPeeileRkKeaf 517
                                           EvR+PflD++l+e+a+ ++p  lk  + ++K+lL+++a+++lP +    +K++f
  FitnessBrowser__Korea:Ga0059261_3119 496 EVRAPFLDHRLIEFAFgKVPSRLKATASDKKILLKQLAARVLPPQFDRQRKQGF 549
                                           **************9868***************************988899998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (616 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 32.21
//
[ok]

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

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Protein sequences (fasta format)
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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