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

GapMind for Amino acid biosynthesis

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

Align Putative asparagine synthetase [glutamine-hydrolyzing]; EC 6.3.5.4 (characterized)
to candidate WP_011383678.1 AMB_RS06425 asparagine synthase (glutamine-hydrolyzing)

Query= SwissProt::P64248
         (652 letters)



>NCBI__GCF_000009985.1:WP_011383678.1
          Length = 585

 Score =  303 bits (777), Expect = 1e-86
 Identities = 230/642 (35%), Positives = 303/642 (47%), Gaps = 89/642 (13%)

Query: 1   MCGLLAFVAAPAGAAGPEGADAASAIARASHLMRHRGPDESGTWHAVDGASGGVVFGFNR 60
           MCG+       AG     G      + + +  + HRGPD  G        SG V    NR
Sbjct: 1   MCGI-------AGVMTANGPPDGQVLDKLADALAHRGPDGRGRH-----VSGNVGLVQNR 48

Query: 61  LSIIDIAHSHQPLRWGPPEAPDRYVLVFNGEIYNYLELRDELRTQHGAVFATDGDGEAIL 120
           LSIID+    QP+  G   A     +V NGEIYNYLEL+ ++    G VFAT  D E  L
Sbjct: 49  LSIIDLEGGRQPILDGAGNA-----IVANGEIYNYLELKSDMA---GQVFATGSDCEPPL 100

Query: 121 AGYHHWGTEVLQRLRGMFAFALWDTVTRELFCARDPFGIKPLFIATGAGGTAVASEKKCL 180
             Y H G    + LRGM+AFA+ D   ++L   RDPFGIKPL++   A G A ASE + L
Sbjct: 101 HLYRHQGPAFARSLRGMYAFAIHDGGAQKLVLGRDPFGIKPLYLTETAPGLAFASEPQAL 160

Query: 181 LDLVELVGFDTEIDHRALQHYTVLQYVPEPETLHRGVRRL--------ESGCFARIRADQ 232
           +    LV    E+D  AL     LQ+     T+ +G+RRL        E GC    R   
Sbjct: 161 I-AAGLV--KPELDPAALAELLQLQFTTGTRTIFKGIRRLGAGETVVAEGGCVTEGRRLP 217

Query: 233 LAPVITRYFVPRFAASPITNDNDQARYDEITAVLEDSVAKHMRADVTVGAFLSGGIDSTA 292
             P          A  P+    DQ   D++   L +SV  H R+DV  G FLSGGIDS+ 
Sbjct: 218 ALP----------AGGPVDGGLDQM-LDQLDDTLTESVELHQRSDVPYGMFLSGGIDSSV 266

Query: 293 IAALAIRHNPR-LITFTTGFE-REGFSEIDVAVASAEAIGARHIAKVVSADEFVAALPEI 350
           + AL  R NP+ ++ FT GF       E   A   A A+GARH+    +  +F   LP +
Sbjct: 267 VLALMARLNPKGVLAFTAGFPGTRVHDERQHARDLARAVGARHVEVEFTESDFWELLPLV 326

Query: 351 VWYLDEPVADPALVPLFFVAREARKHVKVVLSGEGADELFGGYTIYREPLSLRPFDYLPK 410
              +D+P AD A +P F +AREARK VKV+LSGEG DELFGGY  YR   ++RP+     
Sbjct: 327 AAAMDDPAADYACLPTFKLAREARKEVKVILSGEGGDELFGGYGRYRH--AMRPW----- 379

Query: 411 PLRRSMGKVSKPLPEGMRGKSLLHRGSLTLEERYYGNARSFSGAQLREVLPGFRPDWTHT 470
                      PL + MR K                   +F G  L  +  G    W H 
Sbjct: 380 -----------PLTKSMRRKG------------------TFDG--LDVLRDGITSHWRHG 408

Query: 471 DVTAPVYAESAGWDPVARMQHIDLFTWLRGDILVKADKITMANSLELRVPFLDPEVFAVA 530
              A       G   +   Q +D   WL  D+L KAD+  MAN +E RVPFLDP V A A
Sbjct: 409 MKLAERAEALPGRTRLQVAQAVDCTDWLPNDLLTKADRCLMANGIEGRVPFLDPVVAAFA 468

Query: 531 SRLPAGAKITRTTTKYALRRALEPIVPAHVLHRPKLGFPVPIRHWLRA-GELLEWAYATV 589
            RLP   K+ +   K+ LRR LE  +PA      K GF VP+  W+ A  ++ +      
Sbjct: 469 FRLPDHLKVRKGLGKWILRRWLETALPAARPFDKKRGFTVPVAEWIAAKPQIGQLVARQP 528

Query: 590 GSSQAGHLVDIAAVYRMLDEHRCGSSDHSRRLWTMLIFMLWH 631
           G ++  H   + A++R        + D     WT+L + LWH
Sbjct: 529 GIAEICHPGAVEALFRTC------AKDTGFACWTLLFYALWH 564


Lambda     K      H
   0.323    0.138    0.428 

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: 1036
Number of extensions: 51
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: 652
Length of database: 585
Length adjustment: 37
Effective length of query: 615
Effective length of database: 548
Effective search space:   337020
Effective search space used:   337020
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (25.0 bits)

Align candidate WP_011383678.1 AMB_RS06425 (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.26322.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-127  412.8   0.0   1.6e-127  412.6   0.0    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011383678.1  AMB_RS06425 asparagine synthase 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011383678.1  AMB_RS06425 asparagine synthase (glutamine-hydrolyzing)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  412.6   0.0  1.6e-127  1.6e-127       1     517 []       2     506 ..       2     506 .. 0.89

  Alignments for each domain:
  == domain 1  score: 412.6 bits;  conditional E-value: 1.6e-127
                                 TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsnek 69 
                                               Cgiag+++++   +   + +++++++lahRGPD++g + +    n++l+++RL+iidl++g+QP+ + +
  lcl|NCBI__GCF_000009985.1:WP_011383678.1   2 CGIAGVMTANGPPD--GQVLDKLADALAHRGPDGRGRHVS---GNVGLVQNRLSIIDLEGGRQPILDGA 65 
                                               *********88654..58******************7766...9**********************999 PP

                                 TIGR01536  70 evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelfl 138
                                                ++iv nGEIYN+ eL+ ++   G  F t sD+E  L++y++ g ++   L+Gm+Afa++d  +++l+l
  lcl|NCBI__GCF_000009985.1:WP_011383678.1  66 GNAIVANGEIYNYLELKSDMA--GQVFATGSDCEPPLHLYRHQGPAFARSLRGMYAFAIHDGGAQKLVL 132
                                               89***************9887..88******************************************** PP

                                 TIGR01536 139 aRDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepak 207
                                                RD++GikPLY ++++  l+faSE +al+a+  +k+eld +alaell+lq+++  +t+fk++++l +++
  lcl|NCBI__GCF_000009985.1:WP_011383678.1 133 GRDPFGIKPLYLTETAPGLAFASEPQALIAAGLVKPELDPAALAELLQLQFTTGTRTIFKGIRRLGAGE 201
                                               ***************999********************************999**************** PP

                                 TIGR01536 208 al..dgeekleeywevekee......vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslv 268
                                                +  +g    e    ++ ++      v+  ++++ ++l+++l+++v+ + ++dvp+g++lSGG+DSs+v
  lcl|NCBI__GCF_000009985.1:WP_011383678.1 202 TVvaEGGCVTEG---RRLPAlpaggpVDGGLDQMLDQLDDTLTESVELHQRSDVPYGMFLSGGIDSSVV 267
                                               997633333333...222224457779****************************************** PP

                                 TIGR01536 269 aaiakkeaksevktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptai 337
                                                a++++  ++ v  F+ gf++    de ++ar +a+++g +h ev+++e ++ + l+ v  a+++p a+
  lcl|NCBI__GCF_000009985.1:WP_011383678.1 268 LALMARLNPKGVLAFTAGFPGTRVHDERQHARDLARAVGARHVEVEFTESDFWELLPLVAAAMDDPAAD 336
                                               ********************99999******************************************** PP

                                 TIGR01536 338 rasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeealelpeaselaekklllqaklakes 406
                                                a+ p++ l+++ar++ vkV+LsGeG+DElfgGY ++r+a +   l   ++++        + ++    
  lcl|NCBI__GCF_000009985.1:WP_011383678.1 337 YACLPTFKLAREARKE-VKVILSGEGGDELFGGYGRYRHAMRPWPLT--KSMR-------RKGTFDGLD 395
                                               ***************9.**********************85555553..3333.......222222223 PP

                                 TIGR01536 407 elkellkakleeelkekeelkkelkeeseleellrldlelllsdllrak.DrvsmahslEvRvPflDke 474
                                               +l+  +  + ++++k   e +++l+ +++l+ ++  d++ +l+++l+ k Dr++ma+++E RvPflD  
  lcl|NCBI__GCF_000009985.1:WP_011383678.1 396 VLRDGITSHWRHGMKLA-ERAEALPGRTRLQVAQAVDCTDWLPNDLLTKaDRCLMANGIEGRVPFLDPV 463
                                               33333333333333332.344556666999*************************************** PP

                                 TIGR01536 475 lvelalsippelklrdgkeKvlLreaaeellPeeileRkKeaf 517
                                               ++ +a+++p  lk+r+g  K++Lr+ +e+ lP +    kK++f
  lcl|NCBI__GCF_000009985.1:WP_011383678.1 464 VAAFAFRLPDHLKVRKGLGKWILRRWLETALPAARPFDKKRGF 506
                                               ********************************98877777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (585 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: 00:00:00.02
# Mc/sec: 12.77
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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