Alignments for a candidate for asnB in Nitratiruptor tergarcus DSM 16512

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Nitratiruptor tergarcus DSM 16512

Align Putative asparagine synthetase [glutamine-hydrolyzing] 2; EC 6.3.5.4 (uncharacterized)
to candidate WP_084274777.1 B8779_RS01265 asparagine synthase (glutamine-hydrolyzing)

Query= curated2:Q58456
         (515 letters)



>NCBI__GCF_900176045.1:WP_084274777.1
          Length = 570

 Score =  172 bits (435), Expect = 4e-47
 Identities = 128/406 (31%), Positives = 202/406 (49%), Gaps = 56/406 (13%)

Query: 1   MCGINGIIRFGKEVIKEEINKMNKAIKHRGPDDEGIFIYNFKNYSIGLGHVRLAILDLSE 60
           MC I G+I  GK   ++ +N  +  + HRG D+ G++    +   + L H RL IL+   
Sbjct: 1   MCAIFGVI--GKIDREKALNAFS-LLSHRGEDESGVY----EREGVFLAHHRLYILNKDA 53

Query: 61  KGHQPMGYNVDEDKIIYRDDELDRADIIIVYNGEIYNYLELKEKFNLETETGTDTEVILK 120
           K  QP   N                  ++++NGEIYNY    E F+      ++   IL+
Sbjct: 54  K--QPFVQNSK----------------VLLFNGEIYNY----EDFHT-----SEAAAILE 86

Query: 121 LYNKLGFDCVKEFNGMWAFCIFDKKKGLIFCSRDRLGVKPFYYYWDGNEFIFSSELKGIL 180
           +          + +GM+A  + DK+K  ++ +RD  G KP YY +  + FIF+SE+K IL
Sbjct: 87  VAPDFS-----KLDGMFALALLDKEK--LYLARDLFGKKPLYYAFWQDSFIFASEIKAIL 139

Query: 181 AVKEINKKENINKDAVELYFALGFIPSPYSIYKNTFKLEARQNLIFDLDKREIRKYYYWE 240
           A      ++ IN  A+  Y + G +    + Y+  +KL+  + L  D+      K  Y+ 
Sbjct: 140 AY---TNEQKINARALSSYLSFGAVVGRETFYEGIYKLDGGEILELDI------KRLYYA 190

Query: 241 LPDYKPIYDKKKLIEEGKKLLYDAVKIRMRSDVPVGAFLSGGLDSSTVVGVMREFTDLSK 300
              +  +  K+    + K+LL  AVK R++ D P  A LSGG+DSS V  + +       
Sbjct: 191 CKRFTTLLQKRS--GDLKRLLVAAVKKRLQGDFPAVALLSGGVDSSFVSAIAKRLQ--GS 246

Query: 301 LHTFSIGFE-GKYDETPYIKIVVDYFKTQHHHYYFKERDFEELIDKYSWIYDEPFGDYSG 359
           L T+SIG+E G+Y E PY + V  Y  + HH   F + DF   +++ S  +DEP GD + 
Sbjct: 247 LATYSIGYEEGRYSELPYAQEVAQYIGSDHHEIIFTKDDFFATLERASIFFDEPIGDSAS 306

Query: 360 FPTYKVSEMARK-FVTVVLSGDGGDEVFGGYMTHLNGYRMDFIRKL 404
            P + + E  +K    VVLSG+GGDE+F GY  +   + +   R L
Sbjct: 307 LPLFYLMERIKKDGAKVVLSGEGGDEIFLGYRQYFEFFDLYKARDL 352


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: 761
Number of extensions: 60
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: 570
Length adjustment: 35
Effective length of query: 480
Effective length of database: 535
Effective search space:   256800
Effective search space used:   256800
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: 52 (24.6 bits)

Align candidate WP_084274777.1 B8779_RS01265 (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.55704.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     3e-104  335.7   0.0   5.5e-103  331.6   0.0    2.0  1  NCBI__GCF_900176045.1:WP_084274777.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900176045.1:WP_084274777.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  331.6   0.0  5.5e-103  5.5e-103       1     517 []       2     508 ..       2     508 .. 0.85

  Alignments for each domain:
  == domain 1  score: 331.6 bits;  conditional E-value: 5.5e-103
                             TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsnekevvi 73 
                                           C+i+g++ + +      e++ +   +l+hRG D++gv++    e++ l+h+RL i +   ++QP+ +++ +v+
  NCBI__GCF_900176045.1:WP_084274777.1   2 CAIFGVIGKIDR-----EKALNAFSLLSHRGEDESGVYER---EGVFLAHHRLYILNKD-AKQPFVQNS-KVL 64 
                                           999999999553.....44555599************999...7************986.6*******9.5** PP

                             TIGR01536  74 vfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlGik 146
                                            fnGEIYN+e+      ++            iL+         +++L+GmFA+al+d+  ++l+laRD +G+k
  NCBI__GCF_900176045.1:WP_084274777.1  65 LFNGEIYNYEDFHTSEAAA------------ILEVAPD-----FSKLDGMFALALLDK--EKLYLARDLFGKK 118
                                           ***********99544433............6666555.....799************..9************ PP

                             TIGR01536 147 PLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakaldgeeklee.y 218
                                           PLYya  q++++faSEiKa+la    ++++++ al+++l++  v+  +t+++++++l+ ++ l +  ++++ y
  NCBI__GCF_900176045.1:WP_084274777.1 119 PLYYAFWQDSFIFASEIKAILAYT-NEQKINARALSSYLSFGAVVGRETFYEGIYKLDGGEIL-E-LDIKRlY 188
                                           ***********************9.69***************99******************9.3.4444436 PP

                             TIGR01536 219 wevekeevkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeaksevktFsigfedsk 291
                                           +  +  ++++ +++   +l++ll +avkkrl +d p+ +llSGG+DSs+v+aiak+    ++ t+sig+e + 
  NCBI__GCF_900176045.1:WP_084274777.1 189 YACK--RFTTLLQKRSGDLKRLLVAAVKKRLQGDFPAVALLSGGVDSSFVSAIAKRLQG-SLATYSIGYE-EG 257
                                           6654..57777899999***************************************966.9*********.99 PP

                             TIGR01536 292 dldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasiplyllsklarekgvkVvLsGeGa 364
                                            ++e  +a++va+++g++h+e++++++++++ le+    ++ep+ ++as pl+ l+++++++g kVvLsGeG+
  NCBI__GCF_900176045.1:WP_084274777.1 258 RYSELPYAQEVAQYIGSDHHEIIFTKDDFFATLERASIFFDEPIGDSASLPLFYLMERIKKDGAKVVLSGEGG 330
                                           9999********************************************************************* PP

                             TIGR01536 365 DElfgGYeyfreakaeeale...............lpeaselaekkl..................llqaklak 404
                                           DE+f GY  ++e+    +++               +                             + + ++++
  NCBI__GCF_900176045.1:WP_084274777.1 331 DEIFLGYRQYFEFFDLYKARdlkyknwlknyfrsnF----------SpnkewewykrvfsdevifRSSCEVFT 393
                                           ********9999877777765667666555544441..........133334444555555555555556666 PP

                             TIGR01536 405 eselkellkakleeelkekeelkkelkee.....seleellrldlelllsdllrak.DrvsmahslEvRvPfl 471
                                             +++ +l+++++++ + +  +    ++e        + +++ d++  l+ l +ak D +sma  +E+R P+l
  NCBI__GCF_900176045.1:WP_084274777.1 394 DLQKNLFLRQNVKDNESLQVLQPYLEEWErsgwkDGAAFFTYIDIKVRLQSLYLAKlDTTSMAYTIEARTPLL 466
                                           666666666555555444444433333335566577888999*****9999999999**************** PP

                             TIGR01536 472 DkelvelalsippelklrdgkeKvlLreaaeellPeeileRkKeaf 517
                                           D  ++  a+  p+  k      K+lL+++a +++P++i eRkK++f
  NCBI__GCF_900176045.1:WP_084274777.1 467 DSSVLYSAFADPQRSK----APKYLLKKIASKYIPQSIIERKKRGF 508
                                           ********99998666....67**********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (570 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: 9.26
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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Protein sequences (fasta format)
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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