Alignments for a candidate for asnB in Stenotrophomonas chelatiphaga DSM 21508

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Stenotrophomonas chelatiphaga DSM 21508

Align asparagine synthetase B, glutamine-hydrolyzing; EC 6.3.5.4 (characterized)
to candidate WP_057507873.1 ABB28_RS06540 asparagine synthase B

Query= CharProtDB::CH_002444
         (554 letters)



>NCBI__GCF_001431535.1:WP_057507873.1
          Length = 563

 Score =  671 bits (1732), Expect = 0.0
 Identities = 336/561 (59%), Positives = 410/561 (73%), Gaps = 9/561 (1%)

Query: 1   MCSIFGVFDIKT--DAVELRKKALELSRLMRHRGPDWSGIYASDNAILAHERLSIVDVNA 58
           MCSIFG+F ++   D   LR+ ALE S+  RHRGPDWSG+Y  D A+L HERL+IVD   
Sbjct: 1   MCSIFGIFGLQAGDDLPALRRHALESSQRQRHRGPDWSGVYLDDGALLVHERLAIVDPAG 60

Query: 59  GAQPLYNQQKTHVLAVNGEIYNHQALRAEYGDRYQFQTGSDCEVILALYQEKGP-EFLDD 117
           G+QPL ++     LAVNGEIYNHQ L+A     Y FQTGSDCEVI ALY++  P ++L+ 
Sbjct: 61  GSQPLLSEDGGLALAVNGEIYNHQQLKAGLDQPYAFQTGSDCEVINALYRQGEPSQWLER 120

Query: 118 LQGMFAFALYDSEKDAYLIGRDHLGIIPLYMGYDEHGQLYVASEMKALVPVCRTIKEFPA 177
           L G+FAFAL+D      L+ RD +G++PLY G+D  G+L VASE+KALV  C    +FP 
Sbjct: 121 LNGIFAFALWDKAAGRVLVARDPIGVVPLYWGHDAQGRLRVASELKALVDTCADAAQFPP 180

Query: 178 GSYLWSQDGEIRSYYHRDWFDYDAVKDNVTDKNELRQALEDSVKSHLMSDVPYGVLLSGG 237
           G Y  S  G +  YY + W +YDAV+    D  ELR+A E +V+  LMSDVPYGVLLSGG
Sbjct: 181 GHYYDSATGALVRYYQQSWREYDAVQGKPVDLAELREAFERAVERQLMSDVPYGVLLSGG 240

Query: 238 LDSSIISAITKKYAARRVEDQERSEAWWPQLHSFAVGLPGSPDLKAAQEVANHLGTVHHE 297
           LDSS+++A+  +YA RR+ED   SEAWWP+LHSFA+GL GSPDL AA   A  LGTVHH 
Sbjct: 241 LDSSLVAAVAARYARRRIEDGGESEAWWPRLHSFAIGLKGSPDLAAAAIAAEALGTVHHG 300

Query: 298 IHFTVQEGLDAIRDVIYHIETYDVTTIRASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGG 357
             +T +EGLD + +VI HIETYDVTTIRASTPM+L++R+IKAMG+KMVLSGEGSDE+FGG
Sbjct: 301 FEYTFEEGLDVLPEVIRHIETYDVTTIRASTPMFLLARRIKAMGVKMVLSGEGSDEIFGG 360

Query: 358 YLYFHKAPNAKELHEETVRKLLALHMYDCARANKAMSAWGVEARVPFLDKKFLDVAMRIN 417
           YLYFHKAP+A+E H E VRKL ALH YDC RANK+M AWGVE RVPFLD++FLDVAMR +
Sbjct: 361 YLYFHKAPDAREFHSELVRKLDALHNYDCLRANKSMMAWGVEPRVPFLDREFLDVAMRFD 420

Query: 418 PQDKMCGN-----GKMEKHILRECFEAYLPASVAWRQKEQFSDGVGYSWIDTLKEVAAQQ 472
              KM G+      ++EK +LR  FE YLP S+ WRQKEQFSDGVGY WID LK  A  Q
Sbjct: 421 AAHKMVGSEASGGRRVEKGVLRAAFEGYLPESILWRQKEQFSDGVGYGWIDGLKAHAEAQ 480

Query: 473 VSDQQLETARFRFPYNTPTSKEAYLYREIFEELFPLPSAAECVPGGPSVACSSAKAIEWD 532
           VSD+ L  A  RFP+N P +KEAY YR +FE+ FP  +AAE VPGG S+ACSS  AI WD
Sbjct: 481 VSDRVLAAADKRFPHNPPQTKEAYYYRHVFEQYFPSHAAAETVPGGKSIACSSPAAIAWD 540

Query: 533 EAFKKMDDPSGRAV-GVHQSA 552
            +F    DPSGRA+ GVH++A
Sbjct: 541 ASFAAAADPSGRAIAGVHEAA 561


Lambda     K      H
   0.319    0.135    0.407 

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: 932
Number of extensions: 30
Number of successful extensions: 4
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: 554
Length of database: 563
Length adjustment: 36
Effective length of query: 518
Effective length of database: 527
Effective search space:   272986
Effective search space used:   272986
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 (21.8 bits)
S2: 53 (25.0 bits)

Align candidate WP_057507873.1 ABB28_RS06540 (asparagine synthase B)
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.12044.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.6e-130  422.4   0.0   7.6e-110  354.2   0.0    2.7  2  lcl|NCBI__GCF_001431535.1:WP_057507873.1  ABB28_RS06540 asparagine synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057507873.1  ABB28_RS06540 asparagine synthase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  354.2   0.0  7.6e-110  7.6e-110       1     384 [.       2     374 ..       2     385 .. 0.94
   2 !   65.9   0.0   1.9e-22   1.9e-22     439     517 .]     377     461 ..     374     461 .. 0.87

  Alignments for each domain:
  == domain 1  score: 354.2 bits;  conditional E-value: 7.6e-110
                                 TIGR01536   1 Cgiagivdlkakake...eeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPls 66 
                                               C+i+gi+ l+a  +    +++a+++ +++++hRGPD++gv+ d   ++a+l+h+RLai+d  +g QPl 
  lcl|NCBI__GCF_001431535.1:WP_057507873.1   2 CSIFGIFGLQAGDDLpalRRHALES-SQRQRHRGPDWSGVYLD---DGALLVHERLAIVDPAGGSQPLL 66 
                                               9999999998755446555555555.*****************...8********************** PP

                                 TIGR01536  67 nek.evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewg.eelverLeGmFAfalwdekk 133
                                               +e+   ++ +nGEIYNh++L++ l +  y F+t sD+EVi a+y++ +  + +erL+G FAfalwd+++
  lcl|NCBI__GCF_001431535.1:WP_057507873.1  67 SEDgGLALAVNGEIYNHQQLKAGLDQP-YAFQTGSDCEVINALYRQGEpSQWLERLNGIFAFALWDKAA 134
                                               ***999*******************88.***************************************** PP

                                 TIGR01536 134 gelflaRDrlGikPLYyase.qgkllfaSEiKallalk.eikaeldkealaelltlqlvptektlfkev 200
                                               g++++aRD++G+ PLY + + qg+l +aSE+Kal++++ +++++++++++ + ++  +    +++++ +
  lcl|NCBI__GCF_001431535.1:WP_057507873.1 135 GRVLVARDPIGVVPLYWGHDaQGRLRVASELKALVDTCaDAAQFPPGHYYDSATGALV----RYYQQSW 199
                                               ********************9********************************99996....79***** PP

                                 TIGR01536 201 kelepakaldgeekleeywevekeevkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslva 269
                                               +e+++++ + + +                      elre++e+av+++l++dvp+gvllSGGlDSslva
  lcl|NCBI__GCF_001431535.1:WP_057507873.1 200 REYDAVQGK-PVDLA--------------------ELREAFERAVERQLMSDVPYGVLLSGGLDSSLVA 247
                                               ****99997.54433....................49******************************** PP

                                 TIGR01536 270 aiakkeak.............sevktFsigfedskdldeskaarkvadelgtehkevliseeevlkele 325
                                               a+a+++a+              ++++F+ig+++s+dl    aa+ +a++lgt h+ ++ + ee+l+ l+
  lcl|NCBI__GCF_001431535.1:WP_057507873.1 248 AVAARYARrriedggeseawwPRLHSFAIGLKGSPDLA---AAAIAAEALGTVHHGFEYTFEEGLDVLP 313
                                               *******9*************9****************...**************************** PP

                                 TIGR01536 326 evilale..eptairasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeeale 384
                                               evi+++e  ++t+iras+p++ll+++++++gvk+vLsGeG+DE+fgGY yf++a+ +++++
  lcl|NCBI__GCF_001431535.1:WP_057507873.1 314 EVIRHIEtyDVTTIRASTPMFLLARRIKAMGVKMVLSGEGSDEIFGGYLYFHKAPDAREFH 374
                                               **********************************************************998 PP

  == domain 2  score: 65.9 bits;  conditional E-value: 1.9e-22
                                 TIGR01536 439 llrldlelllsdllrakDrvsmahslEvRvPflDkelvelalsippelklr.......dgkeKvlLrea 500
                                               l+r+  +l+ +d+lra+ + +ma+++E RvPflD+e++++a++ ++ +k+        +  eK +Lr a
  lcl|NCBI__GCF_001431535.1:WP_057507873.1 377 LVRKLDALHNYDCLRAN-KSMMAWGVEPRVPFLDREFLDVAMRFDAAHKMVgseasggRRVEKGVLRAA 444
                                               56666678899******.****************************8888654444445679******* PP

                                 TIGR01536 501 aeellPeeileRkKeaf 517
                                               +e++lPe+il+R+Ke+f
  lcl|NCBI__GCF_001431535.1:WP_057507873.1 445 FEGYLPESILWRQKEQF 461
                                               ***************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (563 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: 0.07u 0.01s 00:00:00.08 Elapsed: 00:00:00.09
# Mc/sec: 3.20
//
[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