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 asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate WP_011382552.1 AMB_RS00530 asparagine synthase (glutamine-hydrolyzing)

Query= CharProtDB::CH_005185
         (632 letters)



>NCBI__GCF_000009985.1:WP_011382552.1
          Length = 627

 Score =  277 bits (709), Expect = 9e-79
 Identities = 191/624 (30%), Positives = 324/624 (51%), Gaps = 29/624 (4%)

Query: 1   MCGFVGVFNKHPLAQTADQEELIKQMNQMIVHRGPDSDGYFHDEHVGFGF--RRLSIIDV 58
           MCG  G         TA Q  ++  +   + HRGPD  G + +   G G    RL++ID+
Sbjct: 1   MCGIAGT--------TAAQPAILAGLLARLAHRGPDGQGRWTEPDSGMGLVHARLAVIDL 52

Query: 59  ENGG-QPLSYEDETYWIIFNGEIYNYIELREELEAKGYTFNTDSDTEVLLATYRHYKEEA 117
              G QP+      + + +NGEIYN+ +LR ELEA G  F + SDTEVLL        E 
Sbjct: 53  SQAGAQPMVSPCGRWVLAYNGEIYNHAQLRAELEAVGEHFTSASDTEVLLRLLMRDGVEC 112

Query: 118 ASKLRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTI-NDQVYFASERKSLMVAQN-DIE 175
             +L GMFAF +W++    L  ARD  GIKPL +  +    + FASE  +L      D+ 
Sbjct: 113 LPRLVGMFAFALWDRQTRQLLLARDRVGIKPLVWAALPGGGLAFASEIHALRAVPGIDLS 172

Query: 176 IDKEALQQYMSFQFVPEPSTLDAHVKKVEPGSQFTIRPDGDITFKTYFKANFKPVQTE-E 234
           +D+EAL +Y++  +VP P T+ A ++K+ PGS  +  P    T   +++  +   +   +
Sbjct: 173 LDREALSEYLACLYVPAPRTIHAGIRKLPPGSWLSWSPGKAATIGVWWRPIYGGGRRPGQ 232

Query: 235 DKLVKEVRDAIYDSVNVHMRSDVPVGSFLSGGIDSSFIVS-VAKEFHPSLKTFSVGFEQQ 293
           D+ V+E+   +  +V   + SDV VG FLSGGIDSS + + +A+     ++TF++ F++ 
Sbjct: 233 DEAVEELLPVLRRAVKDCLVSDVQVGCFLSGGIDSSVVAALMAEGAADPVRTFTMTFDEV 292

Query: 294 GFSEVDVAKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADPAAIPLYFVAKEAK 353
            + E + A + AA +G  ++ ++ +     + L  ++  F +P  +P A+ +  +++ A+
Sbjct: 293 HYDEREAAAQVAAHVGSRHV-ELPASSGLADGLDTMIERFGEPFGNPTALLIGDLSRLAR 351

Query: 354 KHVTVALSGEGADELFGGYNIYREPLSLKPFERIPSGLKKMLL-HVAAVMPEGMRGKSLL 412
           +HVTVAL G+G DE+F GY  Y+  L  +    +P  L++ LL  +A ++PE   G+   
Sbjct: 352 QHVTVALVGDGGDEVFAGYPRYQGGLLAERVRLLPGVLRRNLLAPLARMIPERSDGRHAW 411

Query: 413 ERGCTPL-------QDRYIGNAKIFEESVKKQLLKHYNPNLSYRDVTKTYFTESSSYSDI 465
            R    L        + Y    + F  + +++LL+      S        + E  S + +
Sbjct: 412 RRAREFLASTGLDGAETYAAWVEYFSPAERRELLRLARTPAS---PIAARYGEVVSENAL 468

Query: 466 NKMQYVDIHTWMRGDILLKADKMTMANSLELRVPFLDKVVFDVASKIPDELKTKNGTTKY 525
           + MQ  D+ T++ G++L   D M+M ++LELR+P LD  V + A ++   L+   G  K 
Sbjct: 469 DAMQETDLATFLPGNLLAYGDAMSMNHALELRLPLLDHRVIEAAGRLDASLRFAEG-KKT 527

Query: 526 LLRKAAEGIVPEHVLNRKKLGFPVPIRHWLKNEMNEWVRNIIQESQTDAY-IHKDYVLQL 584
           LLR  A  ++P  +++R KLGF  P+  WL+  +   V   +   + +   +    V  +
Sbjct: 528 LLRAVARKLLPRAIVDRPKLGFNPPLGMWLQGPLKAMVAERLTPKRLEELGLAAPAVAAV 587

Query: 585 LEDHCADKADNSRKIWTVLIFMIW 608
           L +    + D+S KIW++L+   W
Sbjct: 588 LAEQAGGRRDHSLKIWSLLVLDAW 611


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: 860
Number of extensions: 46
Number of successful extensions: 8
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: 627
Length adjustment: 38
Effective length of query: 594
Effective length of database: 589
Effective search space:   349866
Effective search space used:   349866
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_011382552.1 AMB_RS00530 (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.3744.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-125  406.1   0.0   1.6e-125  405.9   0.0    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011382552.1  AMB_RS00530 asparagine synthase 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011382552.1  AMB_RS00530 asparagine synthase (glutamine-hydrolyzing)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.9   0.0  1.6e-125  1.6e-125       1     517 []       2     549 ..       2     549 .. 0.88

  Alignments for each domain:
  == domain 1  score: 405.9 bits;  conditional E-value: 1.6e-125
                                 TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsne 68 
                                               Cgiag  +++       + ++ +l +lahRGPD++g w + ++++ +l+h+RLa+idls++ aQP+ + 
  lcl|NCBI__GCF_000009985.1:WP_011382552.1   2 CGIAGTTAAQP------AILAGLLARLAHRGPDGQGRWTE-PDSGMGLVHARLAVIDLSQAgAQPMVSP 63 
                                               99999998866......58899******************.9*****************999******9 PP

                                 TIGR01536  69 k.evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgel 136
                                                 + v+ +nGEIYNh +Lr+ele+ G +F++ sDtEV+L+++   g e++ rL GmFAfalwd+++++l
  lcl|NCBI__GCF_000009985.1:WP_011382552.1  64 CgRWVLAYNGEIYNHAQLRAELEAVGEHFTSASDTEVLLRLLMRDGVECLPRLVGMFAFALWDRQTRQL 132
                                               9999***************************************************************** PP

                                 TIGR01536 137 flaRDrlGikPLYyase.qgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkele 204
                                               +laRDr+GikPL  a   +g l+faSEi al a++ i+ +ld+eal+e+l+  +vp ++t+++++++l+
  lcl|NCBI__GCF_000009985.1:WP_011382552.1 133 LLARDRVGIKPLVWAALpGGGLAFASEIHALRAVPGIDLSLDREALSEYLACLYVPAPRTIHAGIRKLP 201
                                               ************8888879************************************************** PP

                                 TIGR01536 205 pakal....dgeekleeywevekee.vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslv 268
                                               p++ l     +++++  +w+  +   ++  ++e+veel   l++avk  lv+dv+vg++lSGG+DSs+v
  lcl|NCBI__GCF_000009985.1:WP_011382552.1 202 PGSWLswspGKAATIGVWWRPIYGGgRRPGQDEAVEELLPVLRRAVKDCLVSDVQVGCFLSGGIDSSVV 270
                                               ****9986555555666**99998867778999************************************ PP

                                 TIGR01536 269 aaiakkeaksevktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptai 337
                                               aa++++ a+ +v+tF++ f+ + ++de +aa++va+++g++h e+  s+  +++ l+ +i ++ ep+ +
  lcl|NCBI__GCF_000009985.1:WP_011382552.1 271 AALMAEGAADPVRTFTMTFD-EVHYDEREAAAQVAAHVGSRHVELPASS-GLADGLDTMIERFGEPFGN 337
                                               ********************.*********************9998776.58899************** PP

                                 TIGR01536 338 rasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeeale...................... 384
                                               + +     ls+lar++ v+V+L G+G+DE+f+GY +++    +e+++                      
  lcl|NCBI__GCF_000009985.1:WP_011382552.1 338 PTALLIGDLSRLARQH-VTVALVGDGGDEVFAGYPRYQGGLLAERVRllpgvlrrnllaplarmipers 405
                                               ****999*********.******************************9888888888777555533322 PP

                                 TIGR01536 385 .lpeaselaekkl...................llqaklakeselkellkakleeelk.ekeelkkelke 432
                                                                               +++a ++  s  ++    +l ++ +  + +  +e+ +
  lcl|NCBI__GCF_000009985.1:WP_011382552.1 406 dG----------RhawrrareflastgldgaeTYAAWVEYFSPAERRELLRLARTPAsPIAARYGEVVS 464
                                               20..........023333344555555666642222222222222222222333333033444556666 PP

                                 TIGR01536 433 eseleellrldlelllsdllrak.DrvsmahslEvRvPflDkelvelalsippelklrdgkeKvlLrea 500
                                               e++l+++++ dl+++l+++l+a  D +sm h lE+R P+lD++++e+a +++++l++ +g +K lLr +
  lcl|NCBI__GCF_000009985.1:WP_011382552.1 465 ENALDAMQETDLATFLPGNLLAYgDAMSMNHALELRLPLLDHRVIEAAGRLDASLRFAEG-KKTLLRAV 532
                                               69********************99*********************************987.59****** PP

                                 TIGR01536 501 aeellPeeileRkKeaf 517
                                               a++llP++i++R+K +f
  lcl|NCBI__GCF_000009985.1:WP_011382552.1 533 ARKLLPRAIVDRPKLGF 549
                                               **************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (627 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 12.86
//
[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