Alignments for a candidate for asnB in Thiohalomonas denitrificans HLD2

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Thiohalomonas denitrificans HLD2

Align asparagine synthase (glutamine-hydrolysing) 3; EC 6.3.5.4 (characterized)
to candidate WP_092994459.1 BLP65_RS06795 N-acetylglutaminylglutamine amidotransferase

Query= CharProtDB::CH_007942
         (614 letters)



>NCBI__GCF_900102855.1:WP_092994459.1
          Length = 597

 Score =  254 bits (649), Expect = 7e-72
 Identities = 180/582 (30%), Positives = 287/582 (49%), Gaps = 56/582 (9%)

Query: 1   MCGITGWVDFKKQLVQEKQTMDRMTDTLSKRGPDDSNVWGEHHVLFGHKRLAVVDI-EGG 59
           MCGI G + F  Q   +   + RM   L +RGPD    + +  + FGH+RL+++D+ E  
Sbjct: 1   MCGICGELRFDGQ-PPDLGRLGRMLHRLERRGPDHEGSYSDGPLAFGHRRLSIIDLSERS 59

Query: 60  RQPMACTYKGDTYTIIYNGELYNTEDLRKELRARGHQFERTSDTEVLLHSYIEWQEDCVD 119
            QPM          +++NG +YN  +LR+EL+  G +F    DTEV+L +Y  W E CV+
Sbjct: 60  DQPMHDAEL--ELVVVFNGTIYNYPELRRELQGAGFRFFSDGDTEVILKAYAAWGEQCVE 117

Query: 120 HLNGIFAFAVWDEKRNLLFAARDRLGVKPFFYTKEGSSFLFGSEIKAILAHPDIKARVDR 179
            L+G+FAFAVWD +R  LF ARDR G+KP +Y        F S  +A+LA   +   +D 
Sbjct: 118 RLHGMFAFAVWDIRRQRLFLARDRFGIKPLYYALADGELRFASNTQALLASGGVDRDIDP 177

Query: 180 TGLSEIFGLGPSRTPGTGIFKGIKEIRPAHALTF-SKDGLNIWRYWNVESEKH--TDSFD 236
            GL   F L         I KGI+++ P  +++  ++ G+   RYW++ + +     S +
Sbjct: 178 VGLHHQFTLHAVIPAPRTILKGIRKLAPGTSMSIDTEGGVRERRYWDLYASRPPVPRSEE 237

Query: 237 DTVANVRSLFQDAVTRQL-VSDVPVCTFLSGGLDSSAITAIAAGHFEKEGKAPLHTYSID 295
           + +  +    +++V R+L V+DVPV   LSGGLDSS + A+ A    ++G   + T+S+ 
Sbjct: 238 EWLEAIHESLRNSVRRRLEVADVPVGVLLSGGLDSSLLVALLA----EQGVEDILTFSVG 293

Query: 296 YEENDKYFQASAFQPNDDGPWIE---KMTEAFGTTHHKCVISQKDLVDHLEEAVLVKDLP 352
           +E+          QP + G   E    + E +GT HHK  I  + ++  L EAV     P
Sbjct: 294 FED----------QPEEKGSEFEFSDLVVEEYGTRHHKYNIPNEQVLTRLPEAVEQMAEP 343

Query: 353 GMADVDSSLLWFCREIKKDFVVSLSGECADEIFGGYPWFHTADVESGFP--------WMR 404
            +     +       + ++  V  SG+ ADE+FGGY W+   D ESG          + R
Sbjct: 344 MVGQDAVAFYLLGERVSQEVKVVQSGQGADEVFGGYFWYPLMDAESGSDLERFARHYFDR 403

Query: 405 STEERIKLLSDSWQKKLNLKEYVNAKYEETLAETPLLDGETGVDKARRQLFYLNMLWFMT 464
             EE +++++ +++      +Y +   E  LA       +T +D+  R          + 
Sbjct: 404 PHEEFLEMVTPAFRG----GDYTSQSIERLLAAP---GADTFIDRVLRMDV---TTLIVD 453

Query: 465 NLLDRKDRMSMGASLEVRVPFADHRLVEYVWNIPWEMKMHDNRE--KGILRKALEGILPD 522
           + + R D M+M   LE RVPF DH LVE     P  MK+  N +  K  L++   G++PD
Sbjct: 454 DPVKRVDNMTMAWGLEARVPFLDHELVELAMQAPPSMKLGPNGDDHKYALKRIARGLVPD 513

Query: 523 DILYRKKSPYPKTHHPEYTKGVSEWLKTIRSQKDSVLHTLLD 564
            ++ R K  +P              LK +R      +H +LD
Sbjct: 514 AVIDRPKGYFPMPA-----------LKYVRGDFLDFMHDILD 544


Lambda     K      H
   0.320    0.137    0.425 

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: 907
Number of extensions: 48
Number of successful extensions: 6
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: 614
Length of database: 597
Length adjustment: 37
Effective length of query: 577
Effective length of database: 560
Effective search space:   323120
Effective search space used:   323120
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_092994459.1 BLP65_RS06795 (N-acetylglutaminylglutamine amidotransferase)
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.704136.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.9e-139  449.9   0.0   9.1e-139  449.6   0.0    1.0  1  NCBI__GCF_900102855.1:WP_092994459.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900102855.1:WP_092994459.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  449.6   0.0  9.1e-139  9.1e-139       1     516 [.       2     522 ..       2     523 .. 0.91

  Alignments for each domain:
  == domain 1  score: 449.6 bits;  conditional E-value: 9.1e-139
                             TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsnek.ev 71 
                                           Cgi g +  + +   +   + +ml++l++RGPD+eg ++d      ++ghrRL+iidlse  +QP+++++ e 
  NCBI__GCF_900102855.1:WP_092994459.1   2 CGICGELRFDGQPP-DLGRLGRMLHRLERRGPDHEGSYSD---GPLAFGHRRLSIIDLSERsDQPMHDAElEL 70 
                                           9*****99988755.5789******************999...8****************99*********** PP

                             TIGR01536  72 vivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlG 144
                                           v+vfnG IYN+ eLr+el+ +G++F ++ DtEViL+ay +wge++verL+GmFAfa+wd ++++lflaRDr+G
  NCBI__GCF_900102855.1:WP_092994459.1  71 VVVFNGTIYNYPELRRELQGAGFRFFSDGDTEVILKAYAAWGEQCVERLHGMFAFAVWDIRRQRLFLARDRFG 143
                                           ************************************************************************* PP

                             TIGR01536 145 ikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlq.lvptektlfkevkelepakal....dge 212
                                           ikPLYya  +g+l faS  +alla   +++ +d  +l++++tl+ + p ++t+ k++++l p+ ++    +g 
  NCBI__GCF_900102855.1:WP_092994459.1 144 IKPLYYALADGELRFASNTQALLASGGVDRDIDPVGLHHQFTLHaVIPAPRTILKGIRKLAPGTSMsidtEGG 216
                                           ********************************************8889*****************99974444 PP

                             TIGR01536 213 ekleeywevekee..vkeseeelveelrelledavkkrlv.advpvgvllSGGlDSslvaaiakkeaksevkt 282
                                            + ++yw++  ++  v  seee  e + e l+++v++rl  advpvgvllSGGlDSsl++a+++++  +++ t
  NCBI__GCF_900102855.1:WP_092994459.1 217 VRERRYWDLYASRppVPRSEEEWLEAIHESLRNSVRRRLEvADVPVGVLLSGGLDSSLLVALLAEQGVEDILT 289
                                           44444***9887777999*********************66********************99999999**** PP

                             TIGR01536 283 Fsigfedskdldesk..aarkvadelgtehkevliseeevlkeleevilaleeptairasiplyllsklarek 353
                                           Fs+gfed+++ + s+  +   v++e gt+h+++ i +e+vl  l+e + ++ ep+  ++++  yll ++++++
  NCBI__GCF_900102855.1:WP_092994459.1 290 FSVGFEDQPEEKGSEfeFSDLVVEEYGTRHHKYNIPNEQVLTRLPEAVEQMAEPMVGQDAVAFYLLGERVSQE 362
                                           ******8877765554499****************************************************99 PP

                             TIGR01536 354 gvkVvLsGeGaDElfgGYeyfreakaeealelpeaselaekklllqaklakeselkellkakleeelkekeel 426
                                            vkVv sG+GaDE+fgGY ++  + ae    l + ++     +  ++  ++  e+   + +  +++++++e+l
  NCBI__GCF_900102855.1:WP_092994459.1 363 -VKVVQSGQGADEVFGGYFWYPLMDAESGSDLERFAR-----HYFDRPHEEFLEMVTPAFRGGDYTSQSIERL 429
                                           .**********************98888887555444.....4445555555555555566667788888888 PP

                             TIGR01536 427 kkelkeeseleellrldlelllsdl.lrakDrvsmahslEvRvPflDkelvelalsippelklr..dgkeKvl 496
                                            ++  +++ ++++lr d+++l+ d+ +++ D ++ma++lE+RvPflD+elvela++ pp++kl     ++K+ 
  NCBI__GCF_900102855.1:WP_092994459.1 430 LAAPGADTFIDRVLRMDVTTLIVDDpVKRVDNMTMAWGLEARVPFLDHELVELAMQAPPSMKLGpnGDDHKYA 502
                                           8899999**********9998776626666*********************************9977899*** PP

                             TIGR01536 497 LreaaeellPeeileRkKea 516
                                           L+++a++l+P+++ +R+K  
  NCBI__GCF_900102855.1:WP_092994459.1 503 LKRIARGLVPDAVIDRPKGY 522
                                           *****************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (597 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: 40.61
//
[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