Alignments for a candidate for asnB in Bradyrhizobium sp. BTAi1

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Bradyrhizobium sp. BTAi1

Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate WP_041751063.1 BBTA_RS33775 N-acetylglutaminylglutamine amidotransferase

Query= CharProtDB::CH_005185
         (632 letters)



>NCBI__GCF_000015165.1:WP_041751063.1
          Length = 590

 Score =  268 bits (686), Expect = 4e-76
 Identities = 194/629 (30%), Positives = 314/629 (49%), Gaps = 66/629 (10%)

Query: 1   MCGFVGV--FNKHPLAQTADQEELIKQMNQMIVHRGPDSDGYFHDEHVGFGFRRLSIIDV 58
           MCG  G   ++  PL         + +MN  +  RGPD+ G +    V  G RRLSI+D+
Sbjct: 1   MCGICGEVRYSSPPLLHA------LSRMNDAMQARGPDAAGLYVQGGVALGHRRLSILDL 54

Query: 59  ENGGQ-PLSYEDETYWIIFNGEIYNYIELREELEAKGYTFNTDSDTEVLLATYRHYKEEA 117
               Q P+        I+FNG IYN+ ELR EL+AKGY F +D DTEV+L +Y  + +  
Sbjct: 55  SAAAQQPMIDAAFGLGIVFNGCIYNFRELRTELQAKGYRFFSDGDTEVILKSYHAWGKGC 114

Query: 118 ASKLRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTINDQVYFASERKSLMVAQN-DIEI 176
             + +GMFAF +W ++   +  ARD  GIKPLYY        FAS   +L+ A + D  +
Sbjct: 115 VQRFKGMFAFALWERDSGRVVLARDRLGIKPLYYAEGAGFFRFASSMPALLAAGDVDTSL 174

Query: 177 DKEALQQYMSFQ-FVPEPSTLDAHVKKVEPGSQFTIRPDGDITFKTYFKANF-KPVQTEE 234
           D  AL  + SF   VP P T+   VKK+ P +  TI PDG    + Y+  N  +   T+ 
Sbjct: 175 DPTALHHFFSFHAAVPAPRTILNGVKKLAPATLLTIDPDGTQHRERYWSFNVGEQRPTDR 234

Query: 235 DKLVKEVRDAIYDSVNVHMR----SDVPVGSFLSGGIDSSFIVS-VAKEFHPSLKTFSVG 289
               +E  DA+ D + V +     +DVPVG  LSGG+DSS +V+ ++K  H  ++TFS+G
Sbjct: 235 AMSQEEWSDALLDEMTVAVDRRRVADVPVGVLLSGGLDSSLLVALLSKLGHQDIRTFSIG 294

Query: 290 F---EQQGFSEVDVAKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADPAAIPLY 346
           F   ++    E   +   A   G ++    I  +  +  LP  +    +P+    ++  Y
Sbjct: 295 FDAVDEHSGDEFRYSDIIARTFGTDHEQIRIGGDRALEALPNAIAAMSEPMVSHDSVAFY 354

Query: 347 FVAKEAKKHVTVALSGEGADELFGGYNIYREPLSLKPFERIPSGLKKMLLHVAAVMPEGM 406
            ++ E  K V V  SG+GADE+FGGY+ Y                           P  +
Sbjct: 355 LLSSEVAKRVKVVQSGQGADEVFGGYSWY---------------------------PGFL 387

Query: 407 RGKSLLERGCTPLQDRYIGNAKIFEESVKKQLLKHYNPNLSYRDVT----KTYFTESSSY 462
                + +     Q+ Y      ++    ++LL    P+L   DV+    + +F + +  
Sbjct: 388 AANDAVHQ----YQNAYFD----WQHGDLRRLLA---PDLLGDDVSLELVERFFADHAGV 436

Query: 463 SDINKMQYVDIHTWMRGDILLKADKMTMANSLELRVPFLDKVVFDVASKIPDELKTKNGT 522
           S ++K+  +D    M  D + + D MTMA  LE RVPFLD  V ++A+++P ELK  +G 
Sbjct: 437 SAVDKVLQIDTEIMMVDDPVKRVDNMTMAFGLEARVPFLDHEVVELAARMPAELKVTHG- 495

Query: 523 TKYLLRKAAEGIVPEHVLNRKKLGFPVPIRHWLKNEMNEWVRNII--QESQTDAYIHKDY 580
            K++L++AA   VP  V++R K  FPVP   +L+     +VR+++  +++++     +D+
Sbjct: 496 GKHILKEAARRCVPAEVIDRPKGYFPVPSLRYLRGPFLAYVRDVLSDEKARSRGLYQRDF 555

Query: 581 VLQLLEDHCADKADNSR-KIWTVLIFMIW 608
           +  +L++  A+ +     ++W   +   W
Sbjct: 556 IDHMLQNPEAEMSPKGHSRLWQAGLLEAW 584


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: 859
Number of extensions: 50
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 632
Length of database: 590
Length adjustment: 37
Effective length of query: 595
Effective length of database: 553
Effective search space:   329035
Effective search space used:   329035
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: 53 (25.0 bits)

Align candidate WP_041751063.1 BBTA_RS33775 (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.2269728.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.6e-137  444.4   0.0   4.3e-137  444.1   0.0    1.0  1  NCBI__GCF_000015165.1:WP_041751063.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000015165.1:WP_041751063.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  444.1   0.0  4.3e-137  4.3e-137       1     516 [.       2     519 ..       2     520 .. 0.91

  Alignments for each domain:
  == domain 1  score: 444.1 bits;  conditional E-value: 4.3e-137
                             TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsnek.ev 71 
                                           Cgi g v ++       +a+++m+++++ RGPDa g++ +    +++lghrRL+i dls++ +QP+ +++   
  NCBI__GCF_000015165.1:WP_041751063.1   2 CGICGEVRYSSP--PLLHALSRMNDAMQARGPDAAGLYVQ---GGVALGHRRLSILDLSAAaQQPMIDAAfGL 69 
                                           999999999554..45689******************999...8****************99*********99 PP

                             TIGR01536  72 vivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlG 144
                                            ivfnG IYN++eLr el++kGy+F ++ DtEViL++y++wg+ +v+r++GmFAfalw++ +g+++laRDrlG
  NCBI__GCF_000015165.1:WP_041751063.1  70 GIVFNGCIYNFRELRTELQAKGYRFFSDGDTEVILKSYHAWGKGCVQRFKGMFAFALWERDSGRVVLARDRLG 142
                                           ************************************************************************* PP

                             TIGR01536 145 ikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlq.lvptektlfkevkelepakal....dge 212
                                           ikPLYya+ +g + faS + alla+ +++++ld +al+++++++  vp ++t+ ++vk+l pa  l    dg+
  NCBI__GCF_000015165.1:WP_041751063.1 143 IKPLYYAEGAGFFRFASSMPALLAAGDVDTSLDPTALHHFFSFHaAVPAPRTILNGVKKLAPATLLtidpDGT 215
                                           ********************************************999******************9**99999 PP

                             TIGR01536 213 ekleeywevekee.....vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeaksev 280
                                           +++e+yw+ ++ e     +++s+ee  + l + ++ av++r vadvpvgvllSGGlDSsl++a+++k  ++++
  NCBI__GCF_000015165.1:WP_041751063.1 216 QHRERYWSFNVGEqrptdRAMSQEEWSDALLDEMTVAVDRRRVADVPVGVLLSGGLDSSLLVALLSKLGHQDI 288
                                           99999***99988889999999*************************************************** PP

                             TIGR01536 281 ktFsigfe..dskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasiplyllsklar 351
                                           +tFsigf+  d+++ de ++   +a+ +gt+h+++ i  + +l++l++ i a+ ep+  ++s+  ylls ++ 
  NCBI__GCF_000015165.1:WP_041751063.1 289 RTFSIGFDavDEHSGDEFRYSDIIARTFGTDHEQIRIGGDRALEALPNAIAAMSEPMVSHDSVAFYLLSSEVA 361
                                           *******988899999999****************************************************** PP

                             TIGR01536 352 ekgvkVvLsGeGaDElfgGYeyfreakaeealelpeaselaekklllqaklakeselkellkakl...eeelk 421
                                           ++ vkVv sG+GaDE+fgGY+++  + a++++       +++++   + +   + +l++ll  +l   + +l+
  NCBI__GCF_000015165.1:WP_041751063.1 362 KR-VKVVQSGQGADEVFGGYSWYPGFLAANDAV------HQYQNAYFDWQ---HGDLRRLLAPDLlgdDVSLE 424
                                           **.**********************99988885......22333322221...22223333322200034455 PP

                             TIGR01536 422 ekeelkkelkeeseleellrldlelllsdl.lrakDrvsmahslEvRvPflDkelvelalsippelklrdgke 493
                                            +e+ +++ +  s+++++l+ d+e ++ d+ +++ D ++ma +lE+RvPflD+e+vela+++p+elk+ +g  
  NCBI__GCF_000015165.1:WP_041751063.1 425 LVERFFADHAGVSAVDKVLQIDTEIMMVDDpVKRVDNMTMAFGLEARVPFLDHEVVELAARMPAELKVTHG-G 496
                                           566666667777**************998735556*********************************866.8 PP

                             TIGR01536 494 KvlLreaaeellPeeileRkKea 516
                                           K++L+eaa++ +P e+ +R+K  
  NCBI__GCF_000015165.1:WP_041751063.1 497 KHILKEAARRCVPAEVIDRPKGY 519
                                           ********************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (590 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 22.38
//
[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