Alignments for a candidate for asnB in Mycolicibacterium vanbaalenii PYR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Mycolicibacterium vanbaalenii PYR-1

Align asparagine synthase (glutamine-hydrolysing) 3; EC 6.3.5.4 (characterized)
to candidate WP_011779502.1 MVAN_RS11410 N-acetylglutaminylglutamine amidotransferase

Query= CharProtDB::CH_007942
         (614 letters)



>NCBI__GCF_000015305.1:WP_011779502.1
          Length = 601

 Score =  231 bits (588), Expect = 9e-65
 Identities = 169/550 (30%), Positives = 259/550 (47%), Gaps = 40/550 (7%)

Query: 1   MCGITGWVDFKKQLVQEKQTMDRMTDTLSKRGPDDSNVWGEHHVLFGHKRLAVVDI-EGG 59
           MCG TG V          + +  M + +  RGPD + VW +  V  GH+RL ++D+ E G
Sbjct: 1   MCGATGEVRLDGT-TPNVRAVTAMAEVMVPRGPDSAGVWSQGRVALGHRRLKIIDLSEAG 59

Query: 60  RQPMACTYKGDTYTIIYNGELYNTEDLRKELRARGHQFERTSDTEVLLHSYIEWQEDCVD 119
            QPM     G   TI +NG +YN E LR EL   G++F   SDTEVLL  Y  W +  VD
Sbjct: 60  AQPMVDAELG--LTIAWNGCIYNYEQLRDELSGHGYRFFSHSDTEVLLKGYHHWGDRFVD 117

Query: 120 HLNGIFAFAVWDEKRNLLFAARDRLGVKPFFYTKEGSSFLFGSEIKAILAHPDIKARVDR 179
           HL G+FAFA+ +     +   RDRLG+KP + T+      F S + A+LA  ++  R+D 
Sbjct: 118 HLKGMFAFAIVERDSGRVLLGRDRLGIKPLYLTRTADRVRFASSLPALLAGGEVDTRIDP 177

Query: 180 TGLSEIFGLGPSRTPGTGIFKGIKEIRPAHALTFSKDG-LNIWRYWNVESEKHTD----S 234
             L               I +G++++ PA       DG +    YW  +  +  +    S
Sbjct: 178 VALHHYMTFHSVVPAPRTILRGVEKLPPASLTAIEPDGRITTTTYWEPDFSRREERAGWS 237

Query: 235 FDDTVANVRSLFQDAVTRQLVSDVPVCTFLSGGLDSSAITAIAAGHFEKEGKAPLHTYSI 294
             D    V    + AV R+LV+DVPV   LSGG+DSS I  + A    + G+  L T+SI
Sbjct: 238 EKDWEDAVLESLRVAVKRRLVADVPVGCLLSGGVDSSLIVGLLA----EAGQHGLATFSI 293

Query: 295 DYEENDKYFQASAFQPNDDGPWIEKMTEAFGTTHHKCVISQKDLVDHLEEAVLVKDLPGM 354
                   F++      D+  + + + + FGT HH+  I  + ++  L  A+     P +
Sbjct: 294 G-------FESVGGVAGDEFKYSDIIADRFGTDHHQIRIGTERMLPALGGAIGAMSEPMV 346

Query: 355 ADVDSSLLWFCREIKKDFVVSLSGECADEIFGGYPWFHTADVESGFPWMRSTEERIKLLS 414
           +    +     +E+ K   V  SG+ ADE+F GY W+       G P   S E  +    
Sbjct: 347 SHDCVAFYLLSQEVAKHVKVVQSGQGADEVFAGYHWY----PPMGEPAAASVEGSVASYR 402

Query: 415 DSW--QKKLNLKEYVNAKYEETLAETPLL--------DGETGVDKARRQLFYLNMLWFMT 464
            ++  + +    + V+  Y      + L           +TGVD+A R       +  + 
Sbjct: 403 AAFFDRDRDGYADIVSPGYLAADDPSELFVTEHFARPGAQTGVDRALR---LDTTVMLVD 459

Query: 465 NLLDRKDRMSMGASLEVRVPFADHRLVEYVWNIPWEMK-MHDNREKGILRKALEGILPDD 523
           + + R D M+M   LE RVPF DH LVE     P ++K  HD   KG+L++A   ++P +
Sbjct: 460 DPVKRVDNMTMAWGLEGRVPFLDHELVELAATCPPQLKTAHDG--KGVLKQAARQVIPSE 517

Query: 524 ILYRKKSPYP 533
           ++ R K  +P
Sbjct: 518 VIDRPKGYFP 527


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: 919
Number of extensions: 41
Number of successful extensions: 6
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: 614
Length of database: 601
Length adjustment: 37
Effective length of query: 577
Effective length of database: 564
Effective search space:   325428
Effective search space used:   325428
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_011779502.1 MVAN_RS11410 (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.2249.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.9e-131  423.9   0.0   6.8e-131  423.7   0.0    1.0  1  lcl|NCBI__GCF_000015305.1:WP_011779502.1  MVAN_RS11410 N-acetylglutaminylg


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015305.1:WP_011779502.1  MVAN_RS11410 N-acetylglutaminylglutamine amidotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  423.7   0.0  6.8e-131  6.8e-131       1     516 [.       2     525 ..       2     526 .. 0.89

  Alignments for each domain:
  == domain 1  score: 423.7 bits;  conditional E-value: 6.8e-131
                                 TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsne 68 
                                               Cg +g v l+ ++  + +a+ +m+e++  RGPD+ gvw++    +++lghrRL iidlse+ aQP+ ++
  lcl|NCBI__GCF_000015305.1:WP_011779502.1   2 CGATGEVRLDGTTP-NVRAVTAMAEVMVPRGPDSAGVWSQ---GRVALGHRRLKIIDLSEAgAQPMVDA 66 
                                               88899999877654.4689********************9...8***************999******* PP

                                 TIGR01536  69 k.evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgel 136
                                               +   +i +nG IYN+e+Lr+el  +Gy+F ++sDtEV+L+ y++wg ++v++L+GmFAfa++++ +g++
  lcl|NCBI__GCF_000015305.1:WP_011779502.1  67 ElGLTIAWNGCIYNYEQLRDELSGHGYRFFSHSDTEVLLKGYHHWGDRFVDHLKGMFAFAIVERDSGRV 135
                                               **99***************************************************************** PP

                                 TIGR01536 137 flaRDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlq.lvptektlfkevkele 204
                                               +l RDrlGikPLY +++++++ faS + alla  e+++++d  al++++t++ +vp ++t+ ++v++l+
  lcl|NCBI__GCF_000015305.1:WP_011779502.1 136 LLGRDRLGIKPLYLTRTADRVRFASSLPALLAGGEVDTRIDPVALHHYMTFHsVVPAPRTILRGVEKLP 204
                                               ****************************************************999************** PP

                                 TIGR01536 205 pakal....dgeekleeywevekee....vkeseeelveelrelledavkkrlvadvpvgvllSGGlDS 265
                                               pa+      dg  +  +ywe + ++       se++  + + e l+ avk+rlvadvpvg+llSGG+DS
  lcl|NCBI__GCF_000015305.1:WP_011779502.1 205 PASLTaiepDGRITTTTYWEPDFSRreerAGWSEKDWEDAVLESLRVAVKRRLVADVPVGCLLSGGVDS 273
                                               ***99996666666666***988876666667899999******************************* PP

                                 TIGR01536 266 slvaaiakkeaksevktFsigfe..dskdldeskaarkvadelgtehkevliseeevlkeleevilale 332
                                               sl++ ++++  ++ + tFsigfe  +  + de k+   +ad +gt+h+++ i  e +l +l   i a+ 
  lcl|NCBI__GCF_000015305.1:WP_011779502.1 274 SLIVGLLAEAGQHGLATFSIGFEsvGGVAGDEFKYSDIIADRFGTDHHQIRIGTERMLPALGGAIGAMS 342
                                               ************9**********65566668888*********************************** PP

                                 TIGR01536 333 eptairasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeealelpease.laekklllqa 400
                                               ep+  ++++  ylls+++ ++ vkVv sG+GaDE+f+GY+++  +   +a+ +  +    +++ +  ++
  lcl|NCBI__GCF_000015305.1:WP_011779502.1 343 EPMVSHDCVAFYLLSQEVAKH-VKVVQSGQGADEVFAGYHWYPPMGEPAAASVEGSVAsYRAAFFDRDR 410
                                               *********************.********************998777777643333324444445555 PP

                                 TIGR01536 401 klakeselkellkakleeelkekeelkkelkeeseleellrldlelllsdl.lrakDrvsmahslEvRv 468
                                                  +  ++  +l a+ ++el  +e ++++  +++ ++++lrld++ +l d+ +++ D ++ma++lE Rv
  lcl|NCBI__GCF_000015305.1:WP_011779502.1 411 DGYADIVSPGYLAADDPSELFVTE-HFARPGAQTGVDRALRLDTTVMLVDDpVKRVDNMTMAWGLEGRV 478
                                               666666666777766666665554.4555666688888999988887776526777************* PP

                                 TIGR01536 469 PflDkelvelalsippelklrdgkeKvlLreaaeellPeeileRkKea 516
                                               PflD+elvela++ pp+lk+  ++ K +L++aa++++P+e+ +R+K  
  lcl|NCBI__GCF_000015305.1:WP_011779502.1 479 PFLDHELVELAATCPPQLKTA-HDGKGVLKQAARQVIPSEVIDRPKGY 525
                                               *******************85.789********************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (601 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 9.71
//
[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