Alignments for a candidate for asnB in Desulfatiglans anilini DSM 4660

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Desulfatiglans anilini DSM 4660

Align asparagine synthase (glutamine-hydrolysing) (EC 6.3.5.4) (characterized)
to candidate WP_028321394.1 H567_RS0110675 asparagine synthase B

Query= BRENDA::F2DJ31
         (589 letters)



>NCBI__GCF_000422285.1:WP_028321394.1
          Length = 540

 Score =  317 bits (813), Expect = 6e-91
 Identities = 207/521 (39%), Positives = 292/521 (56%), Gaps = 37/521 (7%)

Query: 1   MCGILAVLGVGDVSLAKRSRIIELSRRLRHRGPDWSGIHSFEDCYLAHQRLAIVDPTSGD 60
           MCGI   +G  D     R     +   L HRGPD  GIH  E+    H RL+IVD   G 
Sbjct: 1   MCGIAGCIGTTDTETVNR-----MLDALGHRGPDDRGIHPRENLVFGHTRLSIVDVAKGH 55

Query: 61  QPLYNEDKTVVVTVNGEIYNHEELKAKLK-SHQFQTGSDCEVIAHLYEEYGEEFVDMLDG 119
           QP+     +  +  NGEIYN  +LK  L+  H F+T SD EVI HLY+E G E V  LDG
Sbjct: 56  QPILANGGSAGIICNGEIYNFRQLKHSLRPKHSFKTDSDTEVILHLYQEKGPECVKELDG 115

Query: 120 MFSFVLLDTRDKTFIAARDAIGICPLYMGWGLDGSVWFSSEMKVLS-DDCERFISFPPGH 178
           MF+F L D  +  F+ ARD IGI PLY G+   G+++F+SE+  ++    +    FP GH
Sbjct: 116 MFAFALFD--NDAFLMARDPIGIKPLYYGY-RQGALYFTSELGAMTLAGVDEVHEFPAGH 172

Query: 179 LYSSKTGGLRRWYNPPWFSESIPSTPYDPLL--IRESFEKAVIKRLMTD--VPFGVLLSG 234
            Y+ ++G +R +  PP   E    T  +P+   IRE+F +AV KRL+ D  VP G   SG
Sbjct: 173 YYTPESGFVRYYDIPP--IEDHLLTDIEPVCRRIRETFVRAVKKRLLADSEVPVGSFCSG 230

Query: 235 GLDSSLVASVVSRHLAETKVARQWGNKLHTFCIGLKG-----SPDLKAAKEVADYLGTVH 289
           GLDSSLVA++ +  +            LHTF +G+K      S D+KAAK  A ++G+ H
Sbjct: 231 GLDSSLVAAIAAEEIP----------NLHTFVVGMKDASGDVSDDVKAAKIAAAHIGSTH 280

Query: 290 HELHFTVQEGIDALEEVIYHIETYDVTTIRASTPMFLMSRKIKSLGVKMVLSGEGSDEIF 349
           HEL FT  E  +AL  VI  +ETYD + +R + P +  + K+ +  V +VL+GEG+DE+F
Sbjct: 281 HELLFTEAEYHEALPLVIQKLETYDPSLVRCAVPCY-FTCKLAARYVTVVLTGEGADELF 339

Query: 350 GGYLYFHKAPNKKELHEETCRKIKALHLYDCLRANKATSAWGLEARVPFLDKNFINVAMD 409
            GY Y    P  K L+ E  R I  LH  +  RA++    + LE RVPFLD + I+++M 
Sbjct: 340 TGYHYMKHFPFDK-LNLEARRCIGNLHNINLQRADRMGMHFNLELRVPFLDVDMIDLSMK 398

Query: 410 LDPECKMIRRDLGRIEKWVLRNAFDDNEKPYLPKHILYRQKEQFSDGVGYSWIDGLKDHA 469
           +  E K+      +IEKW+LR AF+D +  YLP  IL+R K Q++ G G   +   +  A
Sbjct: 399 IPAELKIREHHGAKIEKWILRMAFEDTD--YLPDDILWRYKVQYTQGAGCESLG--EQMA 454

Query: 470 SAHVSDSMMTNASFVYPENTPTTKEAYYYRTVFEKFYPKNA 510
            A +SD          PE   ++KEA YY  +F +F+P+++
Sbjct: 455 EAAMSDEEYLQIRAENPEAVISSKEAAYYFKIFREFHPQDS 495


Lambda     K      H
   0.319    0.136    0.415 

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: 701
Number of extensions: 41
Number of successful extensions: 10
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: 589
Length of database: 540
Length adjustment: 36
Effective length of query: 553
Effective length of database: 504
Effective search space:   278712
Effective search space used:   278712
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_028321394.1 H567_RS0110675 (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.1210351.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     5e-130  420.8   0.1   5.5e-109  351.4   0.0    2.9  2  NCBI__GCF_000422285.1:WP_028321394.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000422285.1:WP_028321394.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  351.4   0.0  5.5e-109  5.5e-109       1     381 [.       2     352 ..       2     360 .. 0.94
   2 !   64.8   0.1     4e-22     4e-22     445     517 .]     362     440 ..     353     440 .. 0.92

  Alignments for each domain:
  == domain 1  score: 351.4 bits;  conditional E-value: 5.5e-109
                             TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsnek.evv 72 
                                           Cgiag++  +++     e++++ml++l hRGPD++g++     en ++gh RL+i+d+ +g+QP+ +++ ++ 
  NCBI__GCF_000422285.1:WP_028321394.1   2 CGIAGCIGTTDT-----ETVNRMLDALGHRGPDDRGIHPR---ENLVFGHTRLSIVDVAKGHQPILANGgSAG 66 
                                           ********9774.....89*****************7666...8************************9999* PP

                             TIGR01536  73 ivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlGi 145
                                           i++nGEIYN+++L++ l+ k ++F+t+sDtEViL++y+e g e+v++L+GmFAfal+d+  +++++aRD++Gi
  NCBI__GCF_000422285.1:WP_028321394.1  67 IICNGEIYNFRQLKHSLRPK-HSFKTDSDTEVILHLYQEKGPECVKELDGMFAFALFDN--DAFLMARDPIGI 136
                                           ********************.**************************************..************ PP

                             TIGR01536 146 kPLYyaseqgkllfaSEiKallalk..eikaeldkealaelltlqlvptektlfkevkelepakaldgeekle 216
                                           kPLYy++ qg+l+f SE+ a++ +   e+++++ ++++++  +++          + ++++p+++    +++e
  NCBI__GCF_000422285.1:WP_028321394.1 137 KPLYYGYRQGALYFTSELGAMTLAGvdEVHEFPAGHYYTPESGFV----------RYYDIPPIEDH-LLTDIE 198
                                           ********************99888889***********999999..........689*****997.666666 PP

                             TIGR01536 217 eywevekeevkeseeelveelrelledavkkrlvad..vpvgvllSGGlDSslvaaiakkeaksevktFsigf 287
                                                           +++++re++ +avkkrl ad  vpvg++ SGGlDSslvaaia++e++ +++tF++g+
  NCBI__GCF_000422285.1:WP_028321394.1 199 P---------------VCRRIRETFVRAVKKRLLADseVPVGSFCSGGLDSSLVAAIAAEEIP-NLHTFVVGM 255
                                           5...............99****************6644899**********************.8******** PP

                             TIGR01536 288 e.dskdld.eskaarkvadelgtehkevliseeevlkeleevilale..eptairasiplyllsklarekgvk 356
                                           +  s d++ + kaa+ +a+++g++h+e+l++e+e+ ++l+ vi +le  +p  +r ++p y+ +kla +  v+
  NCBI__GCF_000422285.1:WP_028321394.1 256 KdASGDVSdDVKAAKIAAAHIGSTHHELLFTEAEYHEALPLVIQKLEtyDPSLVRCAVPCYFTCKLAARY-VT 327
                                           *6566665145799999*****************************************************.** PP

                             TIGR01536 357 VvLsGeGaDElfgGYeyfreakaee 381
                                           VvL+GeGaDElf GY+y +++++++
  NCBI__GCF_000422285.1:WP_028321394.1 328 VVLTGEGADELFTGYHYMKHFPFDK 352
                                           *****************99887765 PP

  == domain 2  score: 64.8 bits;  conditional E-value: 4e-22
                             TIGR01536 445 elllsdllrakDrvsmahslEvRvPflDkelvelalsippelklr....dgkeKvlLreaaee..llPeeile 511
                                            +l++ +l++ Dr+ m   lE+RvPflD ++++l ++ip+elk+r    ++ eK++Lr a+e+  +lP++il+
  NCBI__GCF_000422285.1:WP_028321394.1 362 GNLHNINLQRADRMGMHFNLELRVPFLDVDMIDLSMKIPAELKIRehhgAKIEKWILRMAFEDtdYLPDDILW 434
                                           56788899************************************97777789**********99********* PP

                             TIGR01536 512 RkKeaf 517
                                           R K ++
  NCBI__GCF_000422285.1:WP_028321394.1 435 RYKVQY 440
                                           ***987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (540 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: 8.15
//
[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