GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asnB in Magnetospirillum magneticum AMB-1

Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate WP_043745402.1 AMB_RS20340 asparagine synthase (glutamine-hydrolyzing)

Query= CharProtDB::CH_005185
         (632 letters)



>NCBI__GCF_000009985.1:WP_043745402.1
          Length = 635

 Score =  313 bits (801), Expect = 2e-89
 Identities = 213/640 (33%), Positives = 329/640 (51%), Gaps = 40/640 (6%)

Query: 1   MCGFVGVFNKHPLAQTADQEELIKQMNQMIVHRGPDSDGYFHDEHVG--FGFRRLSIIDV 58
           MCGF G  +      T D+E +++ M   +VHRGPD DG + D+  G   GFRRL+IID+
Sbjct: 1   MCGFAGFLDL--TRATPDRETVVRAMAATLVHRGPDDDGAWVDDDAGVALGFRRLAIIDL 58

Query: 59  E-NGGQPLSYEDETYWIIFNGEIYNYIELREELEAKGYTFNTDSDTEVLLATYRHYKEEA 117
              G QP++  D  + I FNGEIYN+ +LR  L  +   +   SDTEVLL     +  EA
Sbjct: 59  TPQGHQPMTSHDGRWVISFNGEIYNHADLRARL-GESMAWRGHSDTEVLLEAVSAWGIEA 117

Query: 118 A-SKLRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTINDQVYFASERKSLMVAQNDIE- 175
           A +   GMFAF +W++ + VL  ARD FG KPLY+      + F SE K+L         
Sbjct: 118 ALAAFDGMFAFALWDRRERVLTLARDRFGEKPLYWAKAGGSLLFGSELKALRAHPAWTGG 177

Query: 176 IDKEALQQYMSFQFVPEPSTLDAHVKKVEPGSQFTIRPDGDITFKTYFKANFKPVQTEE- 234
           ID++AL  YM   ++P P T+   V K+EPG    +   GDI+ K Y+ A       E+ 
Sbjct: 178 IDRDALALYMRLGWIPAPHTIHPGVFKLEPGHLMRVN-GGDISAKAYWSAADCAAGLEDS 236

Query: 235 -----DKLVKEVRDAIYDSVNVHMRSDVPVGSFLSGGIDSSFIVSVAKEFHPS-LKTFSV 288
                +     + + + +SV + M++DVPVG FLSGGIDSS   ++ ++     + +F++
Sbjct: 237 FAGSAEDAADRLEELLRESVRLRMQADVPVGVFLSGGIDSSATAALMRQLSAEPVHSFTI 296

Query: 289 GFEQQGFSEVDVAKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADPAAIPLYFV 348
           GF+Q G  E   A+  A  LG  +    IS  E + ++ ++   +D+P AD AA+P   +
Sbjct: 297 GFDQAGLDESAHARAVADHLGTLHTEVRISDAEALAQVARLPVLYDEPFADAAALPTALL 356

Query: 349 AKEAKKHVTVALSGEGADELFGGYNIYRE-PLSLKPFERIPSGLKKMLLHVAAVMPEGMR 407
           A+  +K VTVALSG+GADELFGGY IYR  P   +  + +P GL+ +     A+   G+ 
Sbjct: 357 AQVTRKSVTVALSGDGADELFGGYGIYRSIPRDWRRLQGLPDGLRAL----GAMGARGLA 412

Query: 408 G--KSLLERGCTPLQDRYIGNAKIFEE-------SVKKQLLKHYNPNLSYRDVTKTYFTE 458
           G  + L     T  + R     ++  E       S+ + L  HY+      D+       
Sbjct: 413 GPAEGLAALAGTVRKRRSHPGHRLGREAERLEAGSLAELLGLHYSRWRGMSDLVPGAGRA 472

Query: 459 SSSYS--------DINKMQYVDIHTWMRGDILLKADKMTMANSLELRVPFLDKVVFDVAS 510
            S +S        D      +D   ++  D+ +K D+ TM  SLE R+PFL   +   A 
Sbjct: 473 ESLFSAPTPRLHDDALATMVLDAMGYLPDDLCVKTDRATMGASLEARLPFLALDIARFAW 532

Query: 511 KIPDELKTKNGTTKYLLRKAAEGIVPEHVLNRKKLGFPVPIRHWLKNEMNEWVRNIIQES 570
            +P  LK +  T K +LR+    +VP  +++R K+GF VP+R WL   + +W  +++ E 
Sbjct: 533 SLPTSLKIEGETGKAVLRRVLYRLVPRALVDRPKMGFEVPLRRWLNGPLRDWADDLLSEE 592

Query: 571 --QTDAYIHKDYVLQLLEDHCADKADNSRKIWTVLIFMIW 608
             +   +++   V Q   +H +   +   ++W  L+F  W
Sbjct: 593 RLRRQGHLNAALVAQCWREHRSGAKNWQNEMWHALMFQAW 632


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: 851
Number of extensions: 40
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 632
Length of database: 635
Length adjustment: 38
Effective length of query: 594
Effective length of database: 597
Effective search space:   354618
Effective search space used:   354618
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: 54 (25.4 bits)

Align candidate WP_043745402.1 AMB_RS20340 (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.7704.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.9e-146  473.6   0.0     6e-146  473.3   0.0    1.1  1  lcl|NCBI__GCF_000009985.1:WP_043745402.1  AMB_RS20340 asparagine synthase 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_043745402.1  AMB_RS20340 asparagine synthase (glutamine-hydrolyzing)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  473.3   0.0    6e-146    6e-146       1     517 []       2     569 ..       2     569 .. 0.90

  Alignments for each domain:
  == domain 1  score: 473.3 bits;  conditional E-value: 6e-146
                                 TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsne 68 
                                               Cg+ag++dl++++ ++e  +++m+ tl hRGPD++g w d ++++++lg+rRLaiidl  + +QP+ ++
  lcl|NCBI__GCF_000009985.1:WP_043745402.1   2 CGFAGFLDLTRATPDRETVVRAMAATLVHRGPDDDGAWVD-DDAGVALGFRRLAIIDLTPQgHQPMTSH 69 
                                               ***********999999***********************.89***************9888******* PP

                                 TIGR01536  69 k.evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewg.eelverLeGmFAfalwdekkge 135
                                               + + vi fnGEIYNh +Lr++l e  + ++++sDtEV+L+a  +wg e++++ ++GmFAfalwd++++ 
  lcl|NCBI__GCF_000009985.1:WP_043745402.1  70 DgRWVISFNGEIYNHADLRARLGES-MAWRGHSDTEVLLEAVSAWGiEAALAAFDGMFAFALWDRRERV 137
                                               *99999*****************99.******************************************* PP

                                 TIGR01536 136 lflaRDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkele 204
                                               l laRDr+G kPLY a+ +g+llf+SE+Kal a+++ +  +d++ala ++ l + p ++t++ +v++le
  lcl|NCBI__GCF_000009985.1:WP_043745402.1 138 LTLARDRFGEKPLYWAKAGGSLLFGSELKALRAHPAWTGGIDRDALALYMRLGWIPAPHTIHPGVFKLE 206
                                               ********************************************************************* PP

                                 TIGR01536 205 pakal...dgeekleeywevekee......vkeseeelveelrelledavkkrlvadvpvgvllSGGlD 264
                                               p++ +    g+ + + yw++++ +      ++ s e++ ++l+ell+++v+ r+ advpvgv+lSGG+D
  lcl|NCBI__GCF_000009985.1:WP_043745402.1 207 PGHLMrvnGGDISAKAYWSAADCAagledsFAGSAEDAADRLEELLRESVRLRMQADVPVGVFLSGGID 275
                                               ****987445555666****999889999999************************************* PP

                                 TIGR01536 265 SslvaaiakkeaksevktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevilalee 333
                                               Ss+ aa++++ ++++v++F+igf+ ++ ldes++ar+vad+lgt h+ev is +e+l++++++ +  +e
  lcl|NCBI__GCF_000009985.1:WP_043745402.1 276 SSATAALMRQLSAEPVHSFTIGFD-QAGLDESAHARAVADHLGTLHTEVRISDAEALAQVARLPVLYDE 343
                                               ************************.******************************************** PP

                                 TIGR01536 334 ptairasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeeale.................. 384
                                               p+a++a+ p+ ll++ +r+  v+V+LsG+GaDElfgGY ++r  +++  ++                  
  lcl|NCBI__GCF_000009985.1:WP_043745402.1 344 PFADAAALPTALLAQVTRKS-VTVALSGDGADELFGGYGIYRSIPRD--WRrlqglpdglralgamgar 409
                                               ********************.**********************8655..44445999999999888888 PP

                                 TIGR01536 385 ...............lpeaselaekkl.......llqaklakeselkellkakleeelkekeelkkelk 431
                                                              +    +   k+          +a+  ++ +l+ell  ++++ +  ++ + ++  
  lcl|NCBI__GCF_000009985.1:WP_043745402.1 410 glagpaeglaalagtV----R---KRRshpghrlGREAERLEAGSLAELLGLHYSRWRGMSDLVPGAGR 471
                                               8888877755533221....1...111345555533344444555555666666655555555555544 PP

                                 TIGR01536 432 ee...........seleellrldlelllsdllrak.DrvsmahslEvRvPflDkelvelalsippelkl 488
                                               +e            +  +++ ld+  +l+d+l +k Dr++m  slE+R Pfl  +++++a+s+p++lk+
  lcl|NCBI__GCF_000009985.1:WP_043745402.1 472 AEslfsaptprlhDDALATMVLDAMGYLPDDLCVKtDRATMGASLEARLPFLALDIARFAWSLPTSLKI 540
                                               4445666888888777788999999******************************************** PP

                                 TIGR01536 489 rdgkeKvlLreaaeellPeeileRkKeaf 517
                                               + ++ K +Lr+++ +l+P+++++R+K++f
  lcl|NCBI__GCF_000009985.1:WP_043745402.1 541 EGETGKAVLRRVLYRLVPRALVDRPKMGF 569
                                               ***************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (635 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: 00:00:00.02
# Mc/sec: 11.42
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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:

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:

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:

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, or view the source code, or see 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