Alignments for a candidate for asnB in Trichlorobacter lovleyi SZ

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Trichlorobacter lovleyi SZ

Align Putative asparagine synthetase [glutamine-hydrolyzing] 2; EC 6.3.5.4 (uncharacterized)
to candidate WP_012469560.1 GLOV_RS07415 asparagine synthase (glutamine-hydrolyzing)

Query= curated2:Q58456
         (515 letters)



>NCBI__GCF_000020385.1:WP_012469560.1
          Length = 614

 Score =  218 bits (556), Expect = 4e-61
 Identities = 155/404 (38%), Positives = 211/404 (52%), Gaps = 37/404 (9%)

Query: 1   MCGINGII-RFGKEVIKEEINKMNKAIKHRGPDDEGIFIYNFKNYSIGLGHVRLAILDLS 59
           MCGI GI+ R  K    E+I +M K I HRGPD  G+F    +  ++ LGH RLAI+DLS
Sbjct: 1   MCGIAGIVYRNKKSNHSEQIAEMLKLIHHRGPDGMGVF----EAENVVLGHRRLAIIDLS 56

Query: 60  EKGHQPMGYNVDEDKIIYRDDELDRADIIIVYNGEIYNYLELKEKFNLETE---TGTDTE 116
             GHQPM Y             LDR   II +NGEIYNYLELKE+ + +     + +DTE
Sbjct: 57  PSGHQPMCY-------------LDR--FIITFNGEIYNYLELKEELSNKGYYFISTSDTE 101

Query: 117 VILKLYNKLGFDCVKEFNGMWAFCIFDKKKGLIFCSRDRLGVKPFYYYWDGNEFIFSSEL 176
           VIL  Y + G DCV   NGM+AF ++D  +  +F +RDR+G KP YY  + NEF F SE 
Sbjct: 102 VILAAYAEWGEDCVTHLNGMFAFGLYDLLERTLFLARDRVGEKPLYYSKNENEFFFFSEP 161

Query: 177 KGILAVKEINKKENI-NKDAVELYFALGFIPSPYSIYKNTFKLEARQNLIFDLDKREIRK 235
           K +++   I   E I N+ A+  Y    F  S  + +   +KL         L     + 
Sbjct: 162 KQVISSGII---EGIPNEVAIRQYLEYQFTLSAQTFFTGIYKLLPGH--CATLRNGVFKS 216

Query: 236 YYYWELPD----YKPIYDKKKLIEEGKKLLYDAVKIRMRSDVPVGAFLSGGLDSSTV-VG 290
             YW L D    Y   Y + KL    K L+ D++KIR+RSDVPV ++LSGG+DS+ +   
Sbjct: 217 REYWSLADVEVDYSISYAEAKL--RIKNLVEDSLKIRLRSDVPVASYLSGGIDSTIIATS 274

Query: 291 VMREFTDLSKLHTFSIGFEGKYDETPYIKIVVDYFKTQHHHYYFKERDFEELIDKYSWIY 350
             +E + LS  +TF+     ++DE+   ++  D     HH    +  D   L    ++  
Sbjct: 275 AAKELSSLS-TYTFTSKKYPRFDESQNARLTADLIHADHHEIEIENADTLSLWQNSTYFM 333

Query: 351 DEPFGDYSGFPTYKVSEMARKFVTVVLSGDGGDEVFGGYMTHLN 394
           DEP   YS      VS    K   VVL G GGDE+F GY  + N
Sbjct: 334 DEPEVGYSLLSQMAVSREVAKQTKVVLGGQGGDELFFGYAWYSN 377


Lambda     K      H
   0.322    0.144    0.434 

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: 812
Number of extensions: 40
Number of successful extensions: 5
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: 515
Length of database: 614
Length adjustment: 36
Effective length of query: 479
Effective length of database: 578
Effective search space:   276862
Effective search space used:   276862
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 (21.9 bits)
S2: 53 (25.0 bits)

Align candidate WP_012469560.1 GLOV_RS07415 (asparagine synthase (glutamine-hydrolyzing))
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.3097208.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.5e-138  448.2   0.0   4.8e-138  447.3   0.0    1.5  2  NCBI__GCF_000020385.1:WP_012469560.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000020385.1:WP_012469560.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  447.3   0.0  4.8e-138  4.8e-138       1     517 []       2     546 ..       2     546 .. 0.88
   2 ?   -3.5   0.0       0.2       0.2     434     465 ..     568     600 ..     556     601 .. 0.76

  Alignments for each domain:
  == domain 1  score: 447.3 bits;  conditional E-value: 4.8e-138
                             TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsnekevv 72 
                                           Cgiagiv +++k+++ +e+i+eml++++hRGPD+ gv++    en++lghrRLaiidls   +QP+ + ++ +
  NCBI__GCF_000020385.1:WP_012469560.1   2 CGIAGIVYRNKKSNH-SEQIAEMLKLIHHRGPDGMGVFEA---ENVVLGHRRLAIIDLSPSgHQPMCYLDRFI 70 
                                           *********998777.59********************99...7***************888*********** PP

                             TIGR01536  73 ivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlGi 145
                                           i+fnGEIYN+ eL+eel +kGy F ++sDtEViLaay ewge++v +L+GmFAf l+d  +++lflaRDr+G 
  NCBI__GCF_000020385.1:WP_012469560.1  71 ITFNGEIYNYLELKEELSNKGYYFISTSDTEVILAAYAEWGEDCVTHLNGMFAFGLYDLLERTLFLARDRVGE 143
                                           ************************************************************************* PP

                             TIGR01536 146 kPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakal...dgeekl 215
                                           kPLYy++++++++f SE K +++   i+  +++ a+ ++l +q++ + +t+f ++++l p++++   +g  k 
  NCBI__GCF_000020385.1:WP_012469560.1 144 KPLYYSKNENEFFFFSEPKQVISSGIIEGIPNEVAIRQYLEYQFTLSAQTFFTGIYKLLPGHCAtlrNGVFKS 216
                                           *******************************************99*******************877666677 PP

                             TIGR01536 216 eeywevekeevkesee..elveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeaksevktFsig 286
                                           +eyw++++ ev+ s++  e++ ++++l+ed++k rl++dvpv+++lSGG+DS+++a+ a+ke+  ++ t++  
  NCBI__GCF_000020385.1:WP_012469560.1 217 REYWSLADVEVDYSISyaEAKLRIKNLVEDSLKIRLRSDVPVASYLSGGIDSTIIATSAAKELS-SLSTYTFT 288
                                           77********7776661155667789************************************99.8******* PP

                             TIGR01536 287 fedskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasiplyllsklarekgvkVvL 359
                                            ++ + +des+ ar +ad +  +h+e++i++++ l+  ++  + ++ep    +  ++ ++s+++ ++  kVvL
  NCBI__GCF_000020385.1:WP_012469560.1 289 SKKYPRFDESQNARLTADLIHADHHEIEIENADTLSLWQNSTYFMDEPEVGYSLLSQMAVSREVAKQ-TKVVL 360
                                           *******************************************************************.***** PP

                             TIGR01536 360 sGeGaDElfgGYeyfreakaeealelpeaselaekkl.................................llq 399
                                           +G+G+DElf GY+++ +   +  l ++ +++++   +                                 ++ 
  NCBI__GCF_000020385.1:WP_012469560.1 361 GGQGGDELFFGYAWYSNLLLKSFLSFSSVADFKLLDKvkvvisfllnspkrtalrlifdsfksfgrplseIYI 433
                                           ************************9777666333222334455556666666566555554444443333333 PP

                             TIGR01536 400 aklakeselkellkakleeelkekeelkkelkee........seleellrldlelllsdllrakDrvsmahsl 464
                                           ++++    +  l+  k++e                        +l+el + +++++l++ll+++Dr smahsl
  NCBI__GCF_000020385.1:WP_012469560.1 434 DTWRGYGCFSLLQDIKIKE--------------GanspvsgcLKLSELKKFEFNYWLHGLLHVEDRSSMAHSL 492
                                           3333333333333322222..............022344567899**************************** PP

                             TIGR01536 465 EvRvPflDkelvelalsippelklrdgkeKvlLreaaeellPeeileR.kKeaf 517
                                           E+RvP+lD++lve+++s+pp  +++   +K ++  a+ ++lP+++ +  +K+++
  NCBI__GCF_000020385.1:WP_012469560.1 493 ESRVPLLDHRLVEFVFSLPPHFMIDGVLNKKIFIDAFSDILPNHVKNNkQKMGY 546
                                           *********************************************998799886 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 0.2
                             TIGR01536 434 seleellrldlelllsdllrakDrv.smahslE 465
                                           s+ ++++++ + ++  + l+ +Dr   m  slE
  NCBI__GCF_000020385.1:WP_012469560.1 568 SNKSSFIYHFVDYYKMKSLQINDRQlWMLISLE 600
                                           667788999999999999999998515888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (614 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 28.32
//
[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