Alignments for a candidate for asnB in Sulfurimonas denitrificans DSM 1251

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Sulfurimonas denitrificans DSM 1251

Align Putative asparagine synthetase [glutamine-hydrolyzing] 2; EC 6.3.5.4 (uncharacterized)
to candidate WP_011371836.1 SUDEN_RS01010 asparagine synthase (glutamine-hydrolyzing)

Query= curated2:Q58456
         (515 letters)



>NCBI__GCF_000012965.1:WP_011371836.1
          Length = 655

 Score =  213 bits (541), Expect = 2e-59
 Identities = 142/431 (32%), Positives = 225/431 (52%), Gaps = 61/431 (14%)

Query: 1   MCGINGIIRFGKEVIK-EEINKMNKAIKHRGPDDEGIFIYN---------------FKN- 43
           MCGI G++   K  +  E  N M K + HRGPD  G   ++               +KN 
Sbjct: 1   MCGIIGVVSLKKPSLNIEYTNAMIKTLHHRGPDGSGSCFFHTGCRHTKRISFFKAYYKNI 60

Query: 44  ---------YSIGLGHVRLAILDLSEKGHQPMGYNVDEDKIIYRDDELDRADIIIVYNGE 94
                    + +  GH RL+I DLS   HQPM              +L + +I I YNGE
Sbjct: 61  NTNELHPHDWDLFFGHTRLSIQDLSINAHQPMS-------------DLSQ-NIWITYNGE 106

Query: 95  IYNYLELKEKFNL---ETETGTDTEVILKLYNKLGFDCVKEFNGMWAFCIFDKKKGLIFC 151
           IYN+ ELK +  +     ++ +DTEVI+  Y + G +C+K+FNGM+AF ++D  K  +F 
Sbjct: 107 IYNFKELKAELQICGHRFKSNSDTEVIIYSYIEWGIECIKKFNGMFAFALYDNFKKELFL 166

Query: 152 SRDRLGVKPFYYYWDGN-EFIFSSELKGILAVKEINKKENINKDAVELYFALGFIPSPYS 210
           +RDR G+KP YY  + +   +F+SE K IL  K+ + +  ++K A+  YF    I +  +
Sbjct: 167 TRDRYGIKPLYYTLNNDGTLLFASETKSILEYKDYSYE--VDKAALVEYFTFQNIFTDKT 224

Query: 211 IYKNTFKLEARQNLIFDLDKRE--IRKYYYWELPDYKP--IYDKKKLIEEGKKLLYDAVK 266
           +++N   L A   +  +L ++E  ++   YW+    KP  + D+++  EE  +L   AV 
Sbjct: 225 LHENIKLLPAGNYIKINLREKEHSLKTQQYWDFDFTKPLNLKDEREYTEELDRLFTQAVN 284

Query: 267 IRMRSDVPVGAFLSGGLDSSTVVGVMREFTDLSKLHTFSIGF--------EGKYDETPYI 318
            ++ SDV VG++LSGG+DS  +  +  +   +  L TF++GF        E  YDE    
Sbjct: 285 RQLVSDVEVGSYLSGGIDSGAIAAIASK--SIKNLKTFTVGFDLNSASGLELAYDERQKA 342

Query: 319 KIVVDYFKTQHHHYYFKERDFEELIDKYSWIYDEPFGDYSGFPTYKVSEMARKFVTVVLS 378
           + +   FKT+H+    K  D E  +  +++  +EP    S +P Y  +++A KFV VVL+
Sbjct: 343 EYMSYLFKTEHYEMVLKSGDMERCLSDFTYHLEEPRVGQS-YPNYYANKLASKFVKVVLA 401

Query: 379 GDGGDEVFGGY 389
           G G DE+F GY
Sbjct: 402 GTGSDELFAGY 412


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: 952
Number of extensions: 68
Number of successful extensions: 7
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: 655
Length adjustment: 36
Effective length of query: 479
Effective length of database: 619
Effective search space:   296501
Effective search space used:   296501
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_011371836.1 SUDEN_RS01010 (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.3365929.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.3e-133  430.0   0.2   1.7e-131  425.7   0.2    2.0  1  NCBI__GCF_000012965.1:WP_011371836.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000012965.1:WP_011371836.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  425.7   0.2  1.7e-131  1.7e-131       1     517 []       2     587 ..       2     587 .. 0.86

  Alignments for each domain:
  == domain 1  score: 425.7 bits;  conditional E-value: 1.7e-131
                             TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaeg..vwkd........................e.keena 46 
                                           Cgi+g+v lk+ +  + e  ++m++tl+hRGPD++g  ++ +                        + ++ + 
  NCBI__GCF_000012965.1:WP_011371836.1   2 CGIIGVVSLKKPSL-NIEYTNAMIKTLHHRGPDGSGscFF-HtgcrhtkrisffkayyknintnelHpHDWDL 72 
                                           *********87644.6799***************994334.35*********************99768899* PP

                             TIGR01536  47 ilghrRLaiidlseg.aQPlsnek.evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelv 117
                                            +gh RL+i dls   +QP+s+ + + +i++nGEIYN++eL++el+  G++F+++sDtEVi+ +y ewg e++
  NCBI__GCF_000012965.1:WP_011371836.1  73 FFGHTRLSIQDLSINaHQPMSDLSqNIWITYNGEIYNFKELKAELQICGHRFKSNSDTEVIIYSYIEWGIECI 145
                                           *************888******9999*********************************************** PP

                             TIGR01536 118 erLeGmFAfalwdekkgelflaRDrlGikPLYyase.qgkllfaSEiKallalkeikaeldkealaelltlql 189
                                           ++++GmFAfal+d+ k+elfl RDr+GikPLYy+ + +g+llfaSE K++l+ k+   e+dk+al+e++t+q+
  NCBI__GCF_000012965.1:WP_011371836.1 146 KKFNGMFAFALYDNFKKELFLTRDRYGIKPLYYTLNnDGTLLFASETKSILEYKDYSYEVDKAALVEYFTFQN 218
                                           **********************************9999**********************************9 PP

                             TIGR01536 190 vptektlfkevkelepakal.......dgeeklee..ywevekee..vkeseeelveelrelledavkkrlva 251
                                             t+ktl++++k l+++++        +++ k  +  yw+ + ++    ++e+e +eel++l+++av+++lv+
  NCBI__GCF_000012965.1:WP_011371836.1 219 IFTDKTLHENIKLLPAGNYIkinlrekEHSLK--TqqYWDFDFTKplNLKDEREYTEELDRLFTQAVNRQLVS 289
                                           99****************99998885433444..355****9999888889999******************* PP

                             TIGR01536 252 dvpvgvllSGGlDSslvaaiakkeaksevktFsigfe.dskd.....ldeskaarkvadelgtehkevlisee 318
                                           dv+vg++lSGG+DS ++aaia+k +k ++ktF++gf+ +s++     +de + a+ ++  + teh+e+++++ 
  NCBI__GCF_000012965.1:WP_011371836.1 290 DVEVGSYLSGGIDSGAIAAIASKSIK-NLKTFTVGFDlNSASglelaYDERQKAEYMSYLFKTEHYEMVLKSG 361
                                           **************************.8*********87664223336777799999**************** PP

                             TIGR01536 319 evlkeleevilaleeptairasiplyllsklarekgvkVvLsGeGaDElfgGYey.freakaeealelpease 390
                                           ++   l +  ++leep  + +s+p y + kla++  vkVvL G G+DElf+GY + + +a ++ ++   e ++
  NCBI__GCF_000012965.1:WP_011371836.1 362 DMERCLSDFTYHLEEPR-VGQSYPNYYANKLASKF-VKVVLAGTGSDELFAGYPWrYYRAVNNVDFD--EYIN 430
                                           ****************9.999**************.*****************85466666666666..2233 PP

                             TIGR01536 391 ...laekkl....llqaklakes.elkellkakleeelkekeelkkelkeeseleellrldlelllsdllrak 455
                                                 ++l     + + ++  + + k ++ +++ +++ +k+++ + ++ e ++++ l+ +++++l++ll ++
  NCBI__GCF_000012965.1:WP_011371836.1 431 kyyEFWQRLipnrEICKVFKPIWgDVKDVCTRDIFADVFKKHSN-RLTSPEDYVNHSLYFEAKTFLHGLLVVE 502
                                           12222222223322223333333134445555555444433333.3333348999****************** PP

                             TIGR01536 456 DrvsmahslEvRvPflDkelvelalsipp.....................elklr..dgkeKvlLreaaeell 505
                                           D++smahslE RvPflD++lv++  +ip+                     ++k    +++ K +Lre+a +++
  NCBI__GCF_000012965.1:WP_011371836.1 503 DKLSMAHSLETRVPFLDNDLVDFSQQIPVnlklsnlqniismnenetgnkQHKYFqkSNDGKNILRETASRYI 575
                                           *****************************99999999999999999998844443358999************ PP

                             TIGR01536 506 PeeileRkKeaf 517
                                           P++i +  K++f
  NCBI__GCF_000012965.1:WP_011371836.1 576 PNNITTLTKQGF 587
                                           *****9999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (655 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: 9.93
//
[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