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 asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate WP_011371799.1 SUDEN_RS00825 asparagine synthase (glutamine-hydrolyzing)

Query= CharProtDB::CH_005185
         (632 letters)



>NCBI__GCF_000012965.1:WP_011371799.1
          Length = 601

 Score =  265 bits (676), Expect = 6e-75
 Identities = 194/618 (31%), Positives = 316/618 (51%), Gaps = 33/618 (5%)

Query: 1   MCGFVGVFNKHPLAQTADQEELIKQMNQMIVHRGPDSDGYFHDEHVGFGFRRLSIIDVEN 60
           MC   G+  +H        E+  K    ++ HRG D  G    +++ F   +LSI    +
Sbjct: 1   MCAIFGILGEH-------DEKKAKDALALLSHRGGDFCGITQGQNLFFAHHKLSITGTNS 53

Query: 61  -GGQPLSYEDETYWIIFNGEIYNYIELREELEAKGYTFNTDSDTEVLLATYRHYKEEAAS 119
              QP SYE     + FNGEIYNY ELR +L  + + F T S+ EV+ A+Y  +      
Sbjct: 54  DSNQPFSYEK--ILLSFNGEIYNYKELRADLSCE-FNFKTQSEAEVIAASYLKWGVNFVL 110

Query: 120 KLRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTINDQVYFASERKSLMVAQNDIEIDKE 179
            LRGMFA  + +  D +LY  RD  G KPL+Y  +N  + FASE K+L+   + IE+D++
Sbjct: 111 HLRGMFAIALLD--DEILYLFRDRLGKKPLFYLHVNAFI-FASEIKALVPFLHSIEMDED 167

Query: 180 ALQQYMSFQFVPEPSTLDAHVKKVEPGSQFTIRPDGDITFKTYFKA--NFKPVQTEEDKL 237
           AL  Y+SF     P T   ++KK+  G ++ I  D  +  K YF        + T  D+ 
Sbjct: 168 ALLSYLSFLAPTPPFTFFKNIKKLAAG-EYLIFKDSKVEIKRYFDLLDTTPSLITNRDEA 226

Query: 238 VKEVRDAIYDSVNVHMRSDVPVGSFLSGGIDSSFIVSVAKEFHPSLKTFSVGFEQQG-FS 296
           V  V++A+ +++N+ + +DVP+ S LSGGIDS+ I + AK+    ++T+++G+++   + 
Sbjct: 227 VFLVQNALEEAINIRLATDVPMASLLSGGIDSAAINAYAKKASMDIQTYTLGYKEFAKYD 286

Query: 297 EVDVAKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADPAAIPLYFVAKEAKKH- 355
           E   A  +A+ LG++N +  IS  E+      ++   D+PL DPAA+PLY +    KK  
Sbjct: 287 ERQNASLSASLLGVKNRAVEISQREFDESCDIVLDALDEPLNDPAAVPLYLLFGHIKKDG 346

Query: 356 VTVALSGEGADELFGGYNIYREPLSLKPFERIPSG--LKKMLLHVAAVMPEGMRGKSLLE 413
             V LSGEG+DELF GY  Y E L ++    + +   L        ++  E  R K + +
Sbjct: 347 YKVVLSGEGSDELFLGYRQYFEFLDIEKLTNLKNKNWLSGYFHSNFSMNREWERYKRVFD 406

Query: 414 RGCTPLQDRYIG-NAKIFEESVKKQLLKHYNPNLSYRDVTKTYFTESSSYSDINKMQYVD 472
                L  R  G N    +++V  +     N +L Y    +  F  SS   +     Y+D
Sbjct: 407 GS---LLFRTTGENFTDLQKNVSMKRNVRDNESLKYIQNYRETFLASSHSDESIWYSYID 463

Query: 473 IHTWMRGDILLKADKMTMANSLELRVPFLDKVVFDVASKIPDELKTKNGTTKYLLRKAAE 532
           +H +     L K D+++MA+S+E R PFLD  +  +   I  +++  +G TK LL+ A +
Sbjct: 464 LHLFQAEHYLTKLDRLSMAHSIESRTPFLDHKLASLVFSIDPKIRYMDGVTKSLLKSALK 523

Query: 533 GIVPEHVLNRKKLGFPVPIRHWLKNEMNEWVRNIIQESQTDAYIHKDYVLQLLEDHCADK 592
            ++ E +L+R+K GF  P   +L   +     ++I+E      I K    ++L++H    
Sbjct: 524 PMLDEKILSRRKKGFSNPFMEYL---IESKKISLIKEVNEKTGIFKK---EILDEHIKKA 577

Query: 593 ADNSRK--IWTVLIFMIW 608
           A+   K  IW + +  +W
Sbjct: 578 ANGGFKQHIWGLYVLSVW 595


Lambda     K      H
   0.319    0.136    0.403 

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: 968
Number of extensions: 55
Number of successful extensions: 9
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: 632
Length of database: 601
Length adjustment: 37
Effective length of query: 595
Effective length of database: 564
Effective search space:   335580
Effective search space used:   335580
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 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate WP_011371799.1 SUDEN_RS00825 (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.506204.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.8e-123  397.8   0.0   5.6e-123  397.6   0.0    1.0  1  NCBI__GCF_000012965.1:WP_011371799.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000012965.1:WP_011371799.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  397.6   0.0  5.6e-123  5.6e-123       1     517 []       2     538 ..       2     538 .. 0.86

  Alignments for each domain:
  == domain 1  score: 397.6 bits;  conditional E-value: 5.6e-123
                             TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsnekevv 72 
                                           C+i+gi+ ++++     +++k  l +l+hRG D  g+ +    +n  ++h++L+i+  ++  +QP+s+ek  +
  NCBI__GCF_000012965.1:WP_011371799.1   2 CAIFGILGEHDE-----KKAKDALALLSHRGGDFCGITQ---GQNLFFAHHKLSITGTNSDsNQPFSYEK-IL 65 
                                           9*******9885.....566677889**********744...58**************9988********.79 PP

                             TIGR01536  73 ivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlGi 145
                                           + fnGEIYN++eLr++l  + ++F+t+s +EVi a+y +wg ++v +L+GmFA+al+d+  + l+l+RDrlG+
  NCBI__GCF_000012965.1:WP_011371799.1  66 LSFNGEIYNYKELRADLSCE-FNFKTQSEAEVIAASYLKWGVNFVLHLRGMFAIALLDD--EILYLFRDRLGK 135
                                           ******************99.**************************************..************ PP

                             TIGR01536 146 kPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakal...dgeekl 215
                                           kPL+y    ++++faSEiKal+++     e+d++al ++l++   +++ t+fk++k+l ++++l   d++ ++
  NCBI__GCF_000012965.1:WP_011371799.1 136 KPLFYLHV-NAFIFASEIKALVPFL-HSIEMDEDALLSYLSFLAPTPPFTFFKNIKKLAAGEYLifkDSKVEI 206
                                           ******99.88**************.699**************9999*****************999999999 PP

                             TIGR01536 216 eeywevekee..vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeaksevktFsig 286
                                           ++y+++ +++    ++ +e+v  ++++le+a++ rl +dvp+++llSGG+DS ++ a akk +  +++t+++g
  NCBI__GCF_000012965.1:WP_011371799.1 207 KRYFDLLDTTpsLITNRDEAVFLVQNALEEAINIRLATDVPMASLLSGGIDSAAINAYAKKASM-DIQTYTLG 278
                                           99**9988776777789999***************************************99976.9******* PP

                             TIGR01536 287 fedskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasiplyllsklarekgvkVvL 359
                                           +++ +++de + a+  a  lg++++ v+is+ e+ +  + v+ al+ep++++a++plyll+  ++++g+kVvL
  NCBI__GCF_000012965.1:WP_011371799.1 279 YKEFAKYDERQNASLSASLLGVKNRAVEISQREFDESCDIVLDALDEPLNDPAAVPLYLLFGHIKKDGYKVVL 351
                                           ************************************************************************* PP

                             TIGR01536 360 sGeGaDElfgGYeyfreakaeeale...............lpeaselaekkl..................... 396
                                           sGeG+DElf GY  ++e+   e+l                +                                
  NCBI__GCF_000012965.1:WP_011371799.1 352 SGEGSDELFLGYRQYFEFLDIEKLTnlknknwlsgyfhsnF----------Smnrewerykrvfdgsllfrtt 414
                                           *****************999999986667666666555442..........0223333444456677666533 PP

                             TIGR01536 397 ..llqaklakeselkellkakleeelkekeelkkelkee...seleellrldlelllsdllrak.Drvsmahs 463
                                                + l+k++++k+ ++   +e+lk++++  +++ ++    e     + dl+l+  +  + k Dr+smahs
  NCBI__GCF_000012965.1:WP_011371799.1 415 geN-FTDLQKNVSMKRNVR--DNESLKYIQNYRETFLASshsDESIWYSYIDLHLFQAEHYLTKlDRLSMAHS 484
                                           321.122222222222222..23333444444444444422244444568899999888888888******** PP

                             TIGR01536 464 lEvRvPflDkelvelalsippelklrdgkeKvlLreaaeellPeeileRkKeaf 517
                                           +E+R PflD++l++l++si+p+++  dg +K lL++a++ +l e+il R+K++f
  NCBI__GCF_000012965.1:WP_011371799.1 485 IESRTPFLDHKLASLVFSIDPKIRYMDGVTKSLLKSALKPMLDEKILSRRKKGF 538
                                           ***************************************************998 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 27.19
//
[ok]

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

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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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