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] 2; EC 6.3.5.4 (uncharacterized)
to candidate WP_011382566.1 AMB_RS00600 asparagine synthase (glutamine-hydrolyzing)

Query= curated2:Q58456
         (515 letters)



>NCBI__GCF_000009985.1:WP_011382566.1
          Length = 639

 Score =  186 bits (473), Expect = 2e-51
 Identities = 152/482 (31%), Positives = 229/482 (47%), Gaps = 54/482 (11%)

Query: 1   MCGINGIIRFGKEVIKEEI-NKMNKAIKHRGPDDEGIFIYNFKNYSIGLGHVRLAILDLS 59
           MCGI G++R G   ++  +   M  A+ HRGPD  GIF        +GLG+ RLA++D +
Sbjct: 1   MCGIFGMVRGGGRPVESNVLAAMKTALHHRGPDGNGIFAEG----PVGLGNTRLAVVDTA 56

Query: 60  EKGHQPMGYNVDEDKIIYRDDELDRADIIIVYNGEIYNYLELK---EKFNLETETGTDTE 116
             G QP+   +D             +   IVYNGE++N+LEL+   E       T +DTE
Sbjct: 57  G-GSQPV---IDPS-----------SGAAIVYNGELFNHLELRAELESVGWCFRTHSDTE 101

Query: 117 VILKLYNKLGFDCVKEFNGMWAFCIFDKKKGLIFCSRDRLGVKPFYYYWDGNEFIFSSEL 176
           V+L  +   G DCV  FNGM+AF +FD K   +F +RD  G+KP Y     +   F+SE 
Sbjct: 102 VVLAAFCVWGEDCVLRFNGMYAFAVFDPKARRVFIARDPAGIKPLYLTETADGLAFASEA 161

Query: 177 KGILAVKEINKKENINKDAVELYFALGFIPSPYSIYKNTFKLEARQNLIFDLD----KRE 232
           K +L +         +  A+  Y   G++    S +    K  A      DL+    +  
Sbjct: 162 KALLPI----AGRRPDWQALWGYLTYGYMAPDCSPFAGITKFPAGSLAWIDLELPAARLA 217

Query: 233 IRKYYYWELPDYKPIYDKKKLIEEGKKLLYDAVKIRMRSDVPVGAFLSGGLDSSTVV--G 290
           +R Y+        P+ +  + ++    LL  AVK  + SDVPVG FLSGGLDSS V    
Sbjct: 218 VRPYWQPRFGCGAPLAE-GEAVDRLDALLSQAVKHELMSDVPVGLFLSGGLDSSAVAYYA 276

Query: 291 VMREFTDLSKLHTFSIGF-EGKYDETPYIKIVVDYFKTQHHHYYFKERDFEELIDKYSWI 349
             R    +S   +F + F E  +DE+   + V  +   +H    F      E + + +  
Sbjct: 277 ARRHGQAIS---SFGLAFEETTHDESNDARTVARHLGIEHKELMFSPALVREGLRRVTET 333

Query: 350 YDEPFGDYSGFPTYKVSEMARKFVTVVLSGDGGDEVFGGYMTHLNGYRM-DFIRKLPKFL 408
            DEPFGD +  P   +S  AR+ VTVVL+G GGDEV  GY T L  +R+    R+LP  L
Sbjct: 334 MDEPFGDSTVVPLLMLSRFAREHVTVVLTGWGGDEVLAGYPT-LTAHRVASLYRRLPGML 392

Query: 409 RVVGSKLPVKKDLNGIANLYL-----LKEAFRLSLINPEE-------FYAESIKEDAIRP 456
                 +P   D   +++ YL      +   R   + PE+       ++ ++ K   + P
Sbjct: 393 --AHGLVPALVDRLPVSDKYLSFEFKARRFLRGMKLTPEQQHFLWMGYFDDAFKHALLTP 450

Query: 457 EI 458
           ++
Sbjct: 451 DV 452


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: 705
Number of extensions: 35
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: 515
Length of database: 639
Length adjustment: 36
Effective length of query: 479
Effective length of database: 603
Effective search space:   288837
Effective search space used:   288837
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_011382566.1 AMB_RS00600 (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.11534.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.6e-130  422.4   0.0   1.9e-130  422.2   0.0    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011382566.1  AMB_RS00600 asparagine synthase 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011382566.1  AMB_RS00600 asparagine synthase (glutamine-hydrolyzing)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  422.2   0.0  1.9e-130  1.9e-130       1     517 []       2     560 ..       2     560 .. 0.90

  Alignments for each domain:
  == domain 1  score: 422.2 bits;  conditional E-value: 1.9e-130
                                 TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsnek 69 
                                               Cgi+g+v      +e ++ +++m  +l+hRGPD++g++ +     ++lg  RLa++d  +g QP+ + +
  lcl|NCBI__GCF_000009985.1:WP_011382566.1   2 CGIFGMVRGGGRPVE-SNVLAAMKTALHHRGPDGNGIFAE---GPVGLGNTRLAVVDTAGGSQPVIDPS 66 
                                               *********887666.69*********************9...8**********************999 PP

                                 TIGR01536  70 .evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelf 137
                                                 ++iv+nGE++Nh eLr+ele  G  F+t+sDtEV+Laa+  wge++v r++Gm+Afa++d k++++f
  lcl|NCBI__GCF_000009985.1:WP_011382566.1  67 sGAAIVYNGELFNHLELRAELESVGWCFRTHSDTEVVLAAFCVWGEDCVLRFNGMYAFAVFDPKARRVF 135
                                               999****************************************************************** PP

                                 TIGR01536 138 laRDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepa 206
                                               +aRD+ GikPLY +++++ l+faSE+Kall++    +++d +al+ +lt+ + +++ + f+++ +++++
  lcl|NCBI__GCF_000009985.1:WP_011382566.1 136 IARDPAGIKPLYLTETADGLAFASEAKALLPIA--GRRPDWQALWGYLTYGYMAPDCSPFAGITKFPAG 202
                                               ********************************9..69**************99**************** PP

                                 TIGR01536 207 kal.......dgeeklee..ywevekee.vkeseeelveelrelledavkkrlvadvpvgvllSGGlDS 265
                                               + +           +     yw+ +        e e+v++l+ ll +avk  l++dvpvg++lSGGlDS
  lcl|NCBI__GCF_000009985.1:WP_011382566.1 203 SLAwidlelpAARLA--VrpYWQPRFGCgAPLAEGEAVDRLDALLSQAVKHELMSDVPVGLFLSGGLDS 269
                                               *99998775444444..255*****99965567789********************************* PP

                                 TIGR01536 266 slvaaiakkeaksevktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleep 334
                                               s+va  a++ + +++ +F ++fe + + des+ ar va++lg+ehke+++s++ v + l++v  +++ep
  lcl|NCBI__GCF_000009985.1:WP_011382566.1 270 SAVAYYAARRHGQAISSFGLAFE-ETTHDESNDARTVARHLGIEHKELMFSPALVREGLRRVTETMDEP 337
                                               ***********************.9******************************************** PP

                                 TIGR01536 335 tairasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeeale................... 384
                                               + ++ ++pl++ls+ are+ v+VvL+G G+DE+++GY       ++   +                   
  lcl|NCBI__GCF_000009985.1:WP_011382566.1 338 FGDSTVVPLLMLSRFAREH-VTVVLTGWGGDEVLAGYPTLTAHRVASLYRrlpgmlahglvpalvdrlp 405
                                               *******************.******************999988888888999*******999999988 PP

                                 TIGR01536 385 ..............lpease.laekklllqaklakeselkellkakleeelkekeelkkelkee..... 433
                                                             + + ++ + e++++l   +++   ++ ll  +++++++++++l++    +     
  lcl|NCBI__GCF_000009985.1:WP_011382566.1 406 vsdkylsfefkarrFLRGMKlTPEQQHFLWMGYFDDAFKHALLTPDVTAQVAQQDSLAHFAGMAagmae 474
                                               888888877666664444445555565444444455555555555555555555444443333344555 PP

                                 TIGR01536 434 .seleellrldlelllsdllrak.DrvsmahslEvRvPflDkelvelalsippelklrdgkeKvlLrea 500
                                                + ++++++ld+ ++l+++ +++ Dr++ma slE+RvP+l k+++++al +p+ lk+  g+ K lL++a
  lcl|NCBI__GCF_000009985.1:WP_011382566.1 475 pTLTDRIMHLDFRYFLHGNGLFQaDRMTMAASLEARVPLLNKQMLDFALPLPAGLKMAGGTPKGLLKKA 543
                                               599***************999999********************************************* PP

                                 TIGR01536 501 aeellPeeileRkKeaf 517
                                               ++ +lP +il  +K++f
  lcl|NCBI__GCF_000009985.1:WP_011382566.1 544 LAPHLPPAILSKPKKGF 560
                                               **************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (639 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: 11.05
//
[ok]

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