Alignments for a candidate for asnB in Sphingomonas wittichii RW1

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Sphingomonas wittichii RW1

Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate WP_012050222.1 SWIT_RS20430 amidotransferase 1, exosortase A system-associated

Query= CharProtDB::CH_005185
         (632 letters)



>NCBI__GCF_000016765.1:WP_012050222.1
          Length = 633

 Score =  306 bits (783), Expect = 2e-87
 Identities = 202/638 (31%), Positives = 333/638 (52%), Gaps = 52/638 (8%)

Query: 1   MCGFVGVFNKHPLAQTADQEELIKQMNQMIVHRGPDSDGYFHDEHVGFGFRRLSIIDVEN 60
           MCG  G+++        D    ++ M  MI HRGPD  G +    VG G RRLSIID+  
Sbjct: 1   MCGIAGLYHLQTAKPVEDAR--VRAMTDMIAHRGPDGSGVWTGPGVGLGHRRLSIIDLAG 58

Query: 61  GGQPLSYEDETYWIIFNGEIYNYIELREELEAKGYTFNTDSDTEVLLATYRHYKEEAASK 120
           G QP++  D    + +NGE+YNY  +R ELEA G  F T SD+EV++  +R +  +  S+
Sbjct: 59  GAQPMASADGQAMLSYNGEVYNYRAVRAELEALGRAFRTSSDSEVIVEAWRQWGPDCLSR 118

Query: 121 LRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTIND-QVYFASERKSLMV-AQNDIEIDK 178
           L GMFAF I ++    L+ ARD  G+KPL+Y  ++D  V F SE K+L+         D 
Sbjct: 119 LNGMFAFAIHDRERGCLFLARDRLGVKPLFYAELSDGSVAFGSELKALLAHPLLRRSPDF 178

Query: 179 EALQQYMSFQFVPEPSTLDAHVKKVEPGSQFTIRPDG---------DITFKTYFKANFKP 229
            A+  Y+   +VP+ +++ A V K+  G    +R            D++F    K +   
Sbjct: 179 SAVDDYLGLGYVPDDTSIVAGVNKLPAGHYLLLRRGAPLPRPVQWWDVSFADRAKGSRAA 238

Query: 230 VQTEEDKLVKEVRDAIYDSVNVHMRSDVPVGSFLSGGIDSSFIVS-VAKEFHPSLKTFSV 288
           +   E++LV  +R A+ D     M SDVP+G+FLSGG+DSS +V+ +A+    ++KT S+
Sbjct: 239 L---EEELVGIMRAAVTD----RMVSDVPLGAFLSGGVDSSAVVALMAEASRQAVKTCSI 291

Query: 289 GFEQQGFSEVDVAKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADPAAIPLYFV 348
           GF+   F E   A   A     ++ ++++S +++   +  +V  FD+P AD +A+P Y V
Sbjct: 292 GFDHPDFDETRYAAAIAERFATDHRTRIVSADDH-GLVDTLVAAFDEPFADASALPTYRV 350

Query: 349 AKEAKKHVTVALSGEGADELFGGYNIYREPLSLKPFERI----PSGLKKMLLHVAAVM-- 402
           A+ A++ VTVALSG+GADE F G   YR     +  ER+    P G ++ L      +  
Sbjct: 351 AELARETVTVALSGDGADEAFAG---YRRLTFFQAEERVRGLLPLGFRRGLFGTLGRVYP 407

Query: 403 -----PEGMRGKSLLERGCTPLQDRY---IG------NAKIFEESVKKQLLKHYNPNLSY 448
                P+ +R KS LE      ++ Y   +G        +++ +   ++L  H       
Sbjct: 408 KLDRAPQMLRAKSTLEGLGRSSEEAYALAVGVTGPALRRRLYTDRAVRELQGH-----RA 462

Query: 449 RDVTKTYFTESSSYSDINKMQYVDIHTWMRGDILLKADKMTMANSLELRVPFLDKVVFDV 508
            D        + +   +++ QY D+  W+ GDIL K D+ +MA  LE R P LD  + + 
Sbjct: 463 EDRYIAAMRAAPARDALDRAQYADLKIWLPGDILTKVDRTSMAVGLEAREPLLDYRLVEF 522

Query: 509 ASKIPDELKTKNGTTKYLLRKAAEGIVPEHVLNRKKLGFPVPIRHWLKNEMNEWVRNIIQ 568
           A+++P  ++ +  T K+LL++A    +P+ +L R+K+GF  PI  W +  + E  R I +
Sbjct: 523 AARLPVRMRVRGTTGKWLLKQAMRRYLPDDILFRRKMGFVTPISAWFRGPLAEEARRIAR 582

Query: 569 ESQ--TDAYIHKDYVLQLLEDHCADKADNSRKIWTVLI 604
            S     ++     +  ++ +H A + D+ R +W +++
Sbjct: 583 ASSLVETSWFDPAALDAVVAEHQAGRFDHGRLLWQLMM 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: 854
Number of extensions: 36
Number of successful extensions: 5
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: 632
Length of database: 633
Length adjustment: 38
Effective length of query: 594
Effective length of database: 595
Effective search space:   353430
Effective search space used:   353430
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 WP_012050222.1 SWIT_RS20430 (amidotransferase 1, exosortase A system-associated)
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.4681.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.8e-151  491.6   0.0   2.1e-151  491.4   0.0    1.0  1  lcl|NCBI__GCF_000016765.1:WP_012050222.1  SWIT_RS20430 amidotransferase 1,


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016765.1:WP_012050222.1  SWIT_RS20430 amidotransferase 1, exosortase A system-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  491.4   0.0  2.1e-151  2.1e-151       1     517 []       2     561 ..       2     561 .. 0.90

  Alignments for each domain:
  == domain 1  score: 491.4 bits;  conditional E-value: 2.1e-151
                                 TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsnek 69 
                                               Cgiag+ +l+++   e + +++m++++ahRGPD++gvw      +++lghrRL+iidl +gaQP+++++
  lcl|NCBI__GCF_000016765.1:WP_012050222.1   2 CGIAGLYHLQTAKPVEDARVRAMTDMIAHRGPDGSGVWTG---PGVGLGHRRLSIIDLAGGAQPMASAD 67 
                                               *********99988899***********************...7************************* PP

                                 TIGR01536  70 .evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelf 137
                                                ++++ +nGE+YN++++r+ele+ G  F+t sD+EVi++a+++wg ++++rL+GmFAfa++d+++g lf
  lcl|NCBI__GCF_000016765.1:WP_012050222.1  68 gQAMLSYNGEVYNYRAVRAELEALGRAFRTSSDSEVIVEAWRQWGPDCLSRLNGMFAFAIHDRERGCLF 136
                                               *99****************************************************************** PP

                                 TIGR01536 138 laRDrlGikPLYyase.qgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelep 205
                                               laRDrlG+kPL+ya+  +g+++f+SE+Kalla++  ++++d +a+ ++l+l +vp+++++ ++v++l++
  lcl|NCBI__GCF_000016765.1:WP_012050222.1 137 LARDRLGVKPLFYAELsDGSVAFGSELKALLAHPLLRRSPDFSAVDDYLGLGYVPDDTSIVAGVNKLPA 205
                                               **************998**************************************************** PP

                                 TIGR01536 206 akal.....dgeekleeywevekee.vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslv 268
                                               +++l      +  +  ++w+v+     k s  +l eel   +++av+ r+v+dvp+g++lSGG+DSs+v
  lcl|NCBI__GCF_000016765.1:WP_012050222.1 206 GHYLllrrgAPLPRPVQWWDVSFADrAKGSRAALEEELVGIMRAAVTDRMVSDVPLGAFLSGGVDSSAV 274
                                               ****9865544444555*****9875788999999********************************** PP

                                 TIGR01536 269 aaiakkeaksevktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptai 337
                                               +a++++ ++++vkt sigf+ ++d+de+++a+++a+ + t+h++ ++s+++    ++ ++ a++ep+a+
  lcl|NCBI__GCF_000016765.1:WP_012050222.1 275 VALMAEASRQAVKTCSIGFD-HPDFDETRYAAAIAERFATDHRTRIVSADDH-GLVDTLVAAFDEPFAD 341
                                               ********************.***************************9996.6799************ PP

                                 TIGR01536 338 rasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeeale...................... 384
                                               +++ p+y +++lare  v+V+LsG+GaDE f+GY +   ++aee+++                      
  lcl|NCBI__GCF_000016765.1:WP_012050222.1 342 ASALPTYRVAELARET-VTVALSGDGADEAFAGYRRLTFFQAEERVRgllplgfrrglfgtlgrvypkl 409
                                               ****************.*****************************************99999997776 PP

                                 TIGR01536 385 ..lpeaselaekkl..................llqaklakeselkellka.kleeelkekeelkkelke 432
                                                  p++ + +                      ++   l+++  + + +++ + +++  +  +  ++ ++
  lcl|NCBI__GCF_000016765.1:WP_012050222.1 410 drAPQMLRAK---StleglgrsseeayalavgVTGPALRRRLYTDRAVRElQGHRAEDRYIAAMRAAPA 475
                                               6633333322...13445666666666666663333344444333333320223333344444555556 PP

                                 TIGR01536 433 eseleellrldlelllsdllrak.DrvsmahslEvRvPflDkelvelalsippelklrdgkeKvlLrea 500
                                               + +l++++++dl+ +l+++++ k Dr+sma +lE+R P+lD +lve+a+++p+ +++r  + K+lL++a
  lcl|NCBI__GCF_000016765.1:WP_012050222.1 476 RDALDRAQYADLKIWLPGDILTKvDRTSMAVGLEAREPLLDYRLVEFAARLPVRMRVRGTTGKWLLKQA 544
                                               699****************************************************************** PP

                                 TIGR01536 501 aeellPeeileRkKeaf 517
                                               ++++lP++il R+K++f
  lcl|NCBI__GCF_000016765.1:WP_012050222.1 545 MRRYLPDDILFRRKMGF 561
                                               ***************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (633 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 8.99
//
[ok]

This GapMind analysis is from Apr 10 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