Alignments for a candidate for asnB in Methylomonas methanica MC09

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Methylomonas methanica MC09

Align Putative asparagine synthetase [glutamine-hydrolyzing]; EC 6.3.5.4 (characterized)
to candidate WP_013819820.1 METME_RS16155 asparagine synthase (glutamine-hydrolyzing)

Query= SwissProt::P64248
         (652 letters)



>NCBI__GCF_000214665.1:WP_013819820.1
          Length = 668

 Score =  212 bits (540), Expect = 4e-59
 Identities = 192/600 (32%), Positives = 269/600 (44%), Gaps = 48/600 (8%)

Query: 1   MCGLLAFVAAPAGAAGPEGADAASAIARASHLMRHRGPDESGTWHAVDGASGGVVFGFNR 60
           MCG+  F+ A          D  + +A A+ +  HRGPD  G W A DG    V F   R
Sbjct: 1   MCGIAGFIYADRNRP----VDPETLVAMAA-IQYHRGPDGFG-WQARDG----VGFSHAR 50

Query: 61  LSIIDI--AHSHQPLRWGPPEAPDRYVLVFNGEIYNYLELRDELRTQHGAVFATDGDGEA 118
           LSIID+      QP       A  R +L  NGE+Y+Y  LR +L T  G  F +  D E 
Sbjct: 51  LSIIDLNQERGRQPFI----SADGRLMLTQNGELYDYQRLRADL-TARGDRFRSKSDSEL 105

Query: 119 ILAGYHHWGTEV-LQRLRGMFAFALWDTVTRELFCARDPFGIKPLFIATGAGGTAVASEK 177
           IL  Y   G +  L  LRG FAFAL D     +   RD FGIKPL+     GG    SE 
Sbjct: 106 ILHLYPRLGLDASLPHLRGEFAFALHDREQDVVHLVRDRFGIKPLYWTEIDGGLVFGSEL 165

Query: 178 KCLLDLVELVGFDTEIDHRALQHYTVLQYVPEPETLHRGVRRLESGCFARI--RADQLAP 235
           K L    E+     + D   L H  +   VP   T   GV +++ G    I  R  +L  
Sbjct: 166 KVLFAHPEVT---RQFDSAGLYHQLMQTMVPG-STAFAGVHQVKPGHVVSIERRNGRLQI 221

Query: 236 VITRYFVPRFAASPITN-DNDQARY-DEITAVLEDSVAKHMRADVTVGAFLSGGIDSTAI 293
              RY+   F          +Q +Y D +   L ++V   + ADV VG +LSGGIDS +I
Sbjct: 222 SDRRYWDMPFPQEHERGAPGNQTQYIDGVRERLIEAVQLRLEADVPVGCYLSGGIDSCSI 281

Query: 294 AALAIRHNPRLI-TFTTGFEREGFSEIDVAVASAEAIGARHIAKVVSADEFVAALPEIVW 352
             LA       +  FT GF+   + E  +A   A+A GA      + A        E +W
Sbjct: 282 IGLATASTQGAVKAFTIGFDNADYDETPIATEMAQATGADQEILRLDATHLYDHFEETLW 341

Query: 353 YLDEPVADPALVPLFFVAREARK-HVKVVLSGEGADELFGGYTIYREPLSLRPFDYLPKP 411
           + +  + +   V    ++R   +   KVVL+GEG+DELFGGY  +R  + L   D++P  
Sbjct: 342 HTERTIYNTLGVAKLLMSRRVNEIGYKVVLTGEGSDELFGGYPAFRRDMFLHGLDHMPPD 401

Query: 412 LRRSMGKVSKPLPEGMRGKSLLHRGSLTLEERYYGNARSFSGAQLREVLPGFR--PDWTH 469
            RR    +     +   G  L      T+++        F+ + L+  L   R  PD  H
Sbjct: 402 ERREWEAMLAESNKLFTGAMLSED---TIDDPALRAKVGFTPSCLQPWLASARRVPDLLH 458

Query: 470 TDVTAPV--YAESA------------GWDPVARMQHIDLFTWLRGDILV-KADKITMANS 514
            D  A +  Y+  A            G  P+ + Q++ + T L G IL    D++ MANS
Sbjct: 459 PDRRAELAHYSPGAAIAEALDQDALQGRHPLDKAQYVWIKTMLEGQILTWGGDRVDMANS 518

Query: 515 LELRVPFLDPEVFAVASRLPAGAKITRTTTKYALRRALEPIVPAHVLHRPKLGFPVPIRH 574
           +E R PFLD  +   A+ LP   +I   T KY LR A++ ++P  +  R K  F  P  H
Sbjct: 519 MEARPPFLDHHLAEYAATLPPSMRIHGRTEKYVLREAMKGLLPETLYKREKFAFMAPPAH 578


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: 1072
Number of extensions: 65
Number of successful extensions: 7
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: 668
Length adjustment: 38
Effective length of query: 614
Effective length of database: 630
Effective search space:   386820
Effective search space used:   386820
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: 54 (25.4 bits)

Align candidate WP_013819820.1 METME_RS16155 (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.26138.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-133  432.5   0.0   1.8e-133  432.2   0.0    1.1  1  lcl|NCBI__GCF_000214665.1:WP_013819820.1  METME_RS16155 asparagine synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000214665.1:WP_013819820.1  METME_RS16155 asparagine synthase (glutamine-hydrolyzing)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  432.2   0.0  1.8e-133  1.8e-133       1     517 []       2     572 ..       2     572 .. 0.89

  Alignments for each domain:
  == domain 1  score: 432.2 bits;  conditional E-value: 1.8e-133
                                 TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg..aQPlsn 67 
                                               Cgiag++ ++++   + e++ +m+  + hRGPD++g w+   ++++++ h+RL+iidl++   +QP+ +
  lcl|NCBI__GCF_000214665.1:WP_013819820.1   2 CGIAGFIYADRNRPVDPETLVAMAAIQYHRGPDGFG-WQA--RDGVGFSHARLSIIDLNQErgRQPFIS 67 
                                               *********99988899*******************.999..59**************97666*****9 PP

                                 TIGR01536  68 ek.evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewg.eelverLeGmFAfalwdekkg 134
                                               ++ + +++ nGE+Y ++ Lr++l ++G +F++ksD+E+iL++y  +g  + + +L+G+FAfal+d++++
  lcl|NCBI__GCF_000214665.1:WP_013819820.1  68 ADgRLMLTQNGELYDYQRLRADLTARGDRFRSKSDSELILHLYPRLGlDASLPHLRGEFAFALHDREQD 136
                                               999****************************************************************** PP

                                 TIGR01536 135 elflaRDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkel 203
                                                ++l+RDr+GikPLY ++ +g l+f+SE+K+l+a++e+++++d ++l ++l   + ++++t+f++v+++
  lcl|NCBI__GCF_000214665.1:WP_013819820.1 137 VVHLVRDRFGIKPLYWTEIDGGLVFGSELKVLFAHPEVTRQFDSAGLYHQLMQTM-VPGSTAFAGVHQV 204
                                               ***********************************************99998885.79*********** PP

                                 TIGR01536 204 epakal.....dgeeklee..ywevekee.....vkeseeelveelrelledavkkrlvadvpvgvllS 260
                                               +p++++     +g  ++++  yw++  ++        ++ + ++ +re l++av+ rl advpvg++lS
  lcl|NCBI__GCF_000214665.1:WP_013819820.1 205 KPGHVVsierrNGRLQISDrrYWDMPFPQehergAPGNQTQYIDGVRERLIEAVQLRLEADVPVGCYLS 273
                                               ******888764444444477****99988888767789999*************************** PP

                                 TIGR01536 261 GGlDSslvaaiakkeaksevktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevil 329
                                               GG+DS ++  +a +  +++vk F+igf+ ++d+de+ +a ++a+++g + + + +++  + +++ee ++
  lcl|NCBI__GCF_000214665.1:WP_013819820.1 274 GGIDSCSIIGLATASTQGAVKAFTIGFD-NADYDETPIATEMAQATGADQEILRLDATHLYDHFEETLW 341
                                               ****************************.**************************************** PP

                                 TIGR01536 330 aleeptairasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeeale.............. 384
                                               ++e+ + ++  +  +l+s++++e g+kVvL+GeG+DElfgGY  fr+  + + l               
  lcl|NCBI__GCF_000214665.1:WP_013819820.1 342 HTERTIYNTLGVAKLLMSRRVNEIGYKVVLTGEGSDELFGGYPAFRRDMFLHGLDhmppderreweaml 410
                                               ****999****************************************9998888887777766665553 PP

                                 TIGR01536 385 ...lpeaselaekkl................................llqaklakese.lkellkakle 417
                                                             +                                + ++++ +  + +++   a+++
  lcl|NCBI__GCF_000214665.1:WP_013819820.1 411 aesN----------KlftgamlsedtiddpalrakvgftpsclqpwlASARRVPDLLHpDRRAELAHYS 469
                                               3330..........1334444555556677776677777877777664444554444403344445666 PP

                                 TIGR01536 418 eelkekeelkkelkee.seleellrldlelllsdllrak..DrvsmahslEvRvPflDkelvelalsip 483
                                                + +  e+l+++  +  + l+++++  ++++l++ ++    Drv ma+s+E+R PflD++l+e+a+++p
  lcl|NCBI__GCF_000214665.1:WP_013819820.1 470 PGAAIAEALDQDALQGrHPLDKAQYVWIKTMLEGQILTWggDRVDMANSMEARPPFLDHHLAEYAATLP 538
                                               6666666666655554699***************9999889**************************** PP

                                 TIGR01536 484 pelklrdgkeKvlLreaaeellPeeileRkKeaf 517
                                               p+++++  +eK++Lrea+++llPe + +R+K af
  lcl|NCBI__GCF_000214665.1:WP_013819820.1 539 PSMRIHGRTEKYVLREAMKGLLPETLYKREKFAF 572
                                               *******************************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (668 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: 00:00:00.04
# Mc/sec: 8.28
//
[ok]

This GapMind analysis is from Apr 10 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