Alignments for a candidate for asnB in Desulfovibrio oxyclinae DSM 11498

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Desulfovibrio oxyclinae DSM 11498

Align asparagine synthase (glutamine-hydrolysing) 3; EC 6.3.5.4 (characterized)
to candidate WP_018124260.1 B149_RS0105935 asparagine synthase (glutamine-hydrolyzing)

Query= CharProtDB::CH_007942
         (614 letters)



>NCBI__GCF_000375485.1:WP_018124260.1
          Length = 628

 Score =  270 bits (689), Expect = 2e-76
 Identities = 200/628 (31%), Positives = 306/628 (48%), Gaps = 87/628 (13%)

Query: 1   MCGITGWVDFKKQLVQEKQTMDRMTDTLSKRGPDDSNVWGEHHVLFGHKRLAVVDIEG-G 59
           MCGI G +D   +     + +  MTD ++ RGPD   V+       GH+RLA++D+   G
Sbjct: 1   MCGICGILDLSGRNPSH-EALQGMTDAIAHRGPDGEGVFVSGPAGLGHRRLAILDLSPTG 59

Query: 60  RQPMACTYKGD-TYTIIYNGELYNTEDLRKELRARGHQFERTSDTEVLLHSYIEWQEDCV 118
            QPM     GD  ++I YNGELYN  +LR++L  RGH F  TSDTEV+L +Y EW   CV
Sbjct: 60  AQPMRT---GDGRFSISYNGELYNFRELRQDLEHRGHSFRSTSDTEVVLKAYAEWGARCV 116

Query: 119 DHLNGIFAFAVWDEKRNLLFAARDRLGVKPFFYTKEGSSFLFGSEIKAILAHPDIKARVD 178
           +  NG+FAFAVWD++R  LF ARDR G+KP +Y   G +FLFGSE KAILAHP+ +  +D
Sbjct: 117 ERFNGMFAFAVWDDRRRELFLARDRYGIKPLYYAFFGRTFLFGSEQKAILAHPEARREID 176

Query: 179 RTGLSEIFGLGPSRTPGTGIFKGIKEIRPAHALTFSKDG----LNIWRYWN---VESEKH 231
             GL E F      T  T + KG++   P    T   D     L++ RYW+    E + H
Sbjct: 177 FEGLLEYFTFQNFFTDKT-LSKGVRLFHPGCTATLGADAVGGELSLRRYWDFDFTEPDTH 235

Query: 232 TDSFDDTVANVRSLFQDAVTRQLVSDVPVCTFLSGGLDSSAITAIAAGHFEKEGKAPLHT 291
               D+ +  +  LF +AV RQ+VSDV +  +LSGG+DS +I+A+AAG      ++ + +
Sbjct: 236 LTE-DEYLEELDHLFNNAVKRQMVSDVELGAYLSGGIDSGSISAVAAGE-----QSYIKS 289

Query: 292 YSIDYEENDKYFQASAFQPNDDGPWIEKMTEAFGTTHHKCVISQ-------KDLVDHLEE 344
           ++  ++ +        F   D+    E+M+  F T H++ V+          DL  HLEE
Sbjct: 290 FTCGFDLSSASGLELTF---DERATAERMSYMFKTEHYEMVLKAGDMERCLPDLTRHLEE 346

Query: 345 AVLVKDLPGMADVDSSLLWFCREIKKDFV-VSLSGECADEIFGGYPW-FHTADVESGFP- 401
             + +  P          ++  ++   FV V LSG   DE+FGGYPW ++ A V   F  
Sbjct: 347 PRVGQSYPN---------FYAAKLASRFVKVVLSGSGGDELFGGYPWRYYRALVCDDFEH 397

Query: 402 --------WMRSTEERI--KLLSDSWQ--KKLNLKEYVNAKY--EETLAETPLLDGETGV 447
                   W R    R+  ++ +  W   K +  ++     +    TL  TP        
Sbjct: 398 YVDQYYVFWQRLIPNRLIQQVFAPVWSEVKHVWTRDIFCDVFGQRRTLPCTP-------- 449

Query: 448 DKARRQLFYLNMLWFMTNLLDRKDRMSMGASLEVRVPFADHRLVEYVWNIPWEMKMHD-- 505
           ++A     Y     F+  LL  +D++SM   LE RVPF D+ LV++   +P  MK+++  
Sbjct: 450 EQAVNNSLYFEAKTFLHGLLVVEDKLSMAHGLENRVPFLDNDLVDFATKVPVSMKLNNLH 509

Query: 506 ---------------------NREKGILRKALEGILPDDILYRKKSPYPKTHHPEYTKGV 544
                                N  K +LR+     +P+DI    K  +       +    
Sbjct: 510 HVVSMNENEVGPKFKRYFQKTNDGKRLLRRLASRFVPEDITMNIKQGFSAPDASWFKGDS 569

Query: 545 SEWLKTIRSQKDSVLHTLLDRKQLDQLL 572
             ++     + D+ ++  LD   + +L+
Sbjct: 570 IRFVAETLIKNDAAIYEFLDPDAVRKLV 597


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: 1003
Number of extensions: 57
Number of successful extensions: 6
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: 614
Length of database: 628
Length adjustment: 37
Effective length of query: 577
Effective length of database: 591
Effective search space:   341007
Effective search space used:   341007
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_018124260.1 B149_RS0105935 (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.3186027.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.2e-140  454.4   0.0     3e-138  447.9   0.0    2.0  1  NCBI__GCF_000375485.1:WP_018124260.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000375485.1:WP_018124260.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  447.9   0.0    3e-138    3e-138       1     517 []       2     557 ..       2     557 .. 0.86

  Alignments for each domain:
  == domain 1  score: 447.9 bits;  conditional E-value: 3e-138
                             TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsnek.ev 71 
                                           Cgi gi+dl+  + + +ea++ m++++ahRGPD+egv+ +     a+lghrRLai dls   aQP++  + + 
  NCBI__GCF_000375485.1:WP_018124260.1   2 CGICGILDLSGRNPS-HEALQGMTDAIAHRGPDGEGVFVS---GPAGLGHRRLAILDLSPTgAQPMRTGDgRF 70 
                                           *********987555.69**********************...8***************988******999** PP

                             TIGR01536  72 vivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlG 144
                                            i +nGE+YN++eLr++le++G++F+++sDtEV+L+ay ewg ++ver++GmFAfa+wd++++elflaRDr+G
  NCBI__GCF_000375485.1:WP_018124260.1  71 SISYNGELYNFRELRQDLEHRGHSFRSTSDTEVVLKAYAEWGARCVERFNGMFAFAVWDDRRRELFLARDRYG 143
                                           ************************************************************************* PP

                             TIGR01536 145 ikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakal.......d 210
                                           ikPLYya  + ++lf+SE Ka+la++e+++e+d e+l e++t+q+  t+ktl+k+v+ ++p+  +        
  NCBI__GCF_000375485.1:WP_018124260.1 144 IKPLYYAFFGRTFLFGSEQKAILAHPEARREIDFEGLLEYFTFQNFFTDKTLSKGVRLFHPGCTAtlgadavG 216
                                           ********************************************889***************99989998877 PP

                             TIGR01536 211 geekleeywevekee..vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeaksevk 281
                                           ge +l++yw+ + +e  ++ +e+e  eel++l+++avk+++v+dv++g++lSGG+DS +++a+a+ e    +k
  NCBI__GCF_000375485.1:WP_018124260.1 217 GELSLRRYWDFDFTEpdTHLTEDEYLEELDHLFNNAVKRQMVSDVELGAYLSGGIDSGSISAVAAGEQS-YIK 288
                                           7788888*****9996666678999****************************************9977.7** PP

                             TIGR01536 282 tFsigfe.dsk.....dldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasiplyllsk 348
                                           +F+ gf+  s+     ++de + a++++ ++ teh+e+++++ ++   l+++ ++leep  + +s+p + ++k
  NCBI__GCF_000375485.1:WP_018124260.1 289 SFTCGFDlSSAsglelTFDERATAERMSYMFKTEHYEMVLKAGDMERCLPDLTRHLEEPR-VGQSYPNFYAAK 360
                                           ******9544333333589999*************************************9.999********* PP

                             TIGR01536 349 larekgvkVvLsGeGaDElfgGYey.freakaeealelpease..laekkl....llqaklakesel.kellk 413
                                           la++  vkVvLsG G+DElfgGY + + +a +  ++e  ++ +  +  ++l    l+q+ +a  +++ k+++ 
  NCBI__GCF_000375485.1:WP_018124260.1 361 LASRF-VKVVLSGSGGDELFGGYPWrYYRALVCDDFE-HYVDQyyVFWQRLipnrLIQQVFAPVWSEvKHVWT 431
                                           *****.*****************85577777777777.22222332222222333666666666554144444 PP

                             TIGR01536 414 akleeelkekeelkkelkee.....seleellrldlelllsdllrakDrvsmahslEvRvPflDkelvelals 481
                                           +++  ++      ++++ +      +++++ l+ +++++l++ll ++D++smah+lE RvPflD++lv++a +
  NCBI__GCF_000375485.1:WP_018124260.1 432 RDIFCDV------FGQRRTLpctpeQAVNNSLYFEAKTFLHGLLVVEDKLSMAHGLENRVPFLDNDLVDFATK 498
                                           4444333......3333333444558999******************************************** PP

                             TIGR01536 482 ipp......................elklr.dgkeKvlLreaaeellPeeileRkKeaf 517
                                           +p+                      +  ++  ++ K+lLr++a + +Pe+i +  K++f
  NCBI__GCF_000375485.1:WP_018124260.1 499 VPVsmklnnlhhvvsmnenevgpkfKRYFQkTNDGKRLLRRLASRFVPEDITMNIKQGF 557
                                           ***66666666666666665555442222246677888888888888888888877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (628 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: 00:00:00.01
# Mc/sec: 17.37
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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