Alignments for a candidate for asnB in Methanococcus maripaludis C5

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Methanococcus maripaludis C5

Align Putative asparagine synthetase [glutamine-hydrolyzing] 1; EC 6.3.5.4 (uncharacterized)
to candidate WP_011868489.1 MMARC5_RS03660 asparagine synthase (glutamine-hydrolyzing)

Query= curated2:Q58516
         (541 letters)



>NCBI__GCF_000016125.1:WP_011868489.1
          Length = 513

 Score =  624 bits (1609), Expect = 0.0
 Identities = 316/541 (58%), Positives = 407/541 (75%), Gaps = 47/541 (8%)

Query: 1   MCSISGIIVKDNQISA---------KYSIDMMKILKHRGRDNSGLLLDDEVIYFNDFEDV 51
           MCSISGI+ KD + S          K+ I+MMKILKHRG D SG++ DDEV+YF +FEDV
Sbjct: 1   MCSISGIVAKDEEGSGSRSLLDNIQKHVINMMKILKHRGPDYSGMMFDDEVLYFENFEDV 60

Query: 52  EDLEEEMIGNLSLAHNRLAIVGRYGVQPIPNEDETIWLVCNGEIYNYIELREYLKQNHEF 111
            +   E I  +++ HNRLAIVG   VQPIPN+DE+IW++CNGEIYN+IELR+ L   HEF
Sbjct: 61  VE-NTETISRMAMGHNRLAIVGT-AVQPIPNDDESIWIICNGEIYNHIELRDELSVEHEF 118

Query: 112 RTDSDNEVIIHLYEEEKLEELDGDYAFAIYDKSKNVVRLARDMFGVKPLFYVDRDKYFAF 171
           +TD+D+E IIH Y +E ++ LDGDYA+AIYDK KN++ L RD+ GVKPL+++D D+YFAF
Sbjct: 119 KTDTDSEAIIHAYGDELIDVLDGDYAYAIYDKEKNIIELRRDLMGVKPLYFIDMDEYFAF 178

Query: 172 ASERKALWHLLINIDGCERDLDE-LNSKIKTLKPNSQLIYYLDDNRFEIIEGFKKLELNY 230
           ASE+KAL +LL+ I+G  RD     N  I  L PN++L + LD+N + I E  +K+  NY
Sbjct: 179 ASEKKALHYLLMEING--RDYKSAFNYDISRLNPNTRLTFELDENSWYIEEDLEKVNSNY 236

Query: 231 MKERSYEEAKEYLDRALKNSVLKRVRGLDKVGIICSGGVDSSLIAKLASLYCEVILYAVG 290
            +E+ YE  +  L+  + +SV+KRV+GL+KVGII SGGVDS+LI+KLAS YCEVILY+VG
Sbjct: 237 FEEKDYELCRNELETTILDSVMKRVKGLEKVGIIYSGGVDSTLISKLASEYCEVILYSVG 296

Query: 291 TENSEDLIYAERLAKDLNLKLRKKIISEEEYEEYVFKVAKAIDEVDLMKIGVGIPIYVAS 350
           +ENSEDLIYAER AKD+ L  RKKIISE+E+EEYV KVAKAIDE+D+MK+ VGIPI  AS
Sbjct: 297 SENSEDLIYAERAAKDMGLDFRKKIISEDEFEEYVVKVAKAIDELDVMKLSVGIPILAAS 356

Query: 351 EMANEDGLKVVLSGQGADELFGGYARHERIYRERGEEELKKELLKDVYNLYKVNLERDDH 410
           EMA EDG+KV+LSGQGADELF GY R++RI  E+GE+ LK+ ++ DV++++K+NLERDDH
Sbjct: 357 EMAKEDGIKVLLSGQGADELFAGYNRYQRILNEKGEDGLKESIISDVFDIHKINLERDDH 416

Query: 411 CTMANGVELRVPFLDEEVVEIALSIPIEYKMSELSNRPYAESNISLKSEPINGLKNTNLN 470
           CTMANGVELRVPFLD+ V+++ LSIP+EYK+ E                           
Sbjct: 417 CTMANGVELRVPFLDKFVIDVGLSIPVEYKIEE--------------------------- 449

Query: 471 IKCVRSVRKKILRDVASQYLPDYIAYRPKKAAQYGSGGEKMIYKVAKKYGFSKKRINEFL 530
                  RKKILRD+AS+Y+PDYIA RPKKAAQYGSG EKM+Y VAKK+G+SK++INEF 
Sbjct: 450 ------PRKKILRDIASKYVPDYIAQRPKKAAQYGSGSEKMVYAVAKKHGYSKRKINEFF 503

Query: 531 D 531
           +
Sbjct: 504 E 504


Lambda     K      H
   0.318    0.138    0.388 

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: 977
Number of extensions: 51
Number of successful extensions: 6
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: 541
Length of database: 513
Length adjustment: 35
Effective length of query: 506
Effective length of database: 478
Effective search space:   241868
Effective search space used:   241868
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate WP_011868489.1 MMARC5_RS03660 (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.10610.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.9e-111  358.9   6.3    4.8e-90  288.9   3.1    2.0  2  lcl|NCBI__GCF_000016125.1:WP_011868489.1  MMARC5_RS03660 asparagine syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016125.1:WP_011868489.1  MMARC5_RS03660 asparagine synthase (glutamine-hydrolyzing)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  288.9   3.1   4.8e-90   4.8e-90       1     380 [.       2     389 ..       2     393 .. 0.87
   2 !   71.7   0.1   3.1e-24   3.1e-24     435     515 ..     394     474 ..     386     476 .. 0.90

  Alignments for each domain:
  == domain 1  score: 288.9 bits;  conditional E-value: 4.8e-90
                                 TIGR01536   1 Cgiagivdlkakake.......eeeaikemletlahRGPDaegvwkd................ekeena 46 
                                               C+i giv+++++ +         ++ + +m++ l+hRGPD +g+  d                e+ ++ 
  lcl|NCBI__GCF_000016125.1:WP_011868489.1   2 CSISGIVAKDEEGSGsrslldnIQKHVINMMKILKHRGPDYSGMMFDdevlyfenfedvventETISRM 70 
                                               77777777766543333334334688999**************97778************98557899* PP

                                 TIGR01536  47 ilghrRLaiidlsegaQPlsnek.evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewge 114
                                               ++gh+RLai+      QP+ n++ + +i++nGEIYNh eLr+el  + +eF+t++D+E i++ay     
  lcl|NCBI__GCF_000016125.1:WP_011868489.1  71 AMGHNRLAIVGTA--VQPIPNDDeSIWIICNGEIYNHIELRDELSVE-HEFKTDTDSEAIIHAYGD--- 133
                                               **********996..8*******99********************99.***************966... PP

                                 TIGR01536 115 elverLeGmFAfalwdekkgelflaRDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealae 183
                                               el++ L+G++A a++d++k+ + l+RD +G+kPLY+  +++ ++faSE+Kal  l     e+++  +++
  lcl|NCBI__GCF_000016125.1:WP_011868489.1 134 ELIDVLDGDYAYAIYDKEKNIIELRRDLMGVKPLYFIDMDEYFAFASEKKALHYLL---MEINGRDYKS 199
                                               ****************************************************9999...6788888888 PP

                                 TIGR01536 184 lltlq.lvptektlfkevkelepakal...dgeekleeywevekeevkeseeelveelrelledavkkr 248
                                                + +  ++ +++t  +  +el++ +     d e+ +++y+e       ++ e   +el+ ++ d+v kr
  lcl|NCBI__GCF_000016125.1:WP_011868489.1 200 AFNYDiSRLNPNT--RLTFELDENSWYieeDLEKVNSNYFEE------KDYELCRNELETTILDSVMKR 260
                                               8887743333333..333444444443111444444445544......455666689************ PP

                                 TIGR01536 249 lvadvpvgvllSGGlDSslvaaiakkeaksevktFsigfedskdldeskaarkvadelgtehkevlise 317
                                               + +  +vg++ SGG+DS+l++ +a+++ +  v ++s+g e+s+dl    +a+++a+++g++ ++ +ise
  lcl|NCBI__GCF_000016125.1:WP_011868489.1 261 VKGLEKVGIIYSGGVDSTLISKLASEYCE--VILYSVGSENSEDLI---YAERAAKDMGLDFRKKIISE 324
                                               ***************************99..***************...******************** PP

                                 TIGR01536 318 eevlkeleevilale..eptairasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakae 380
                                               +e+ + + +v  a++  ++++ +  ip +++s++a+e+g+kV+LsG+GaDElf+GY+++++  +e
  lcl|NCBI__GCF_000016125.1:WP_011868489.1 325 DEFEEYVVKVAKAIDelDVMKLSVGIPILAASEMAKEDGIKVLLSGQGADELFAGYNRYQRILNE 389
                                               ***************999*****************************************998776 PP

  == domain 2  score: 71.7 bits;  conditional E-value: 3.1e-24
                                 TIGR01536 435 eleellrldlelllsdllrakDrvsmahslEvRvPflDkelvelalsippelklrdgkeKvlLreaaee 503
                                                l+e + +d+  +++ +l+++D ++ma+++E+RvPflDk ++++ lsip+e+k+++  +K +Lr +a +
  lcl|NCBI__GCF_000016125.1:WP_011868489.1 394 GLKESIISDVFDIHKINLERDDHCTMANGVELRVPFLDKFVIDVGLSIPVEYKIEE-PRKKILRDIASK 461
                                               578889999999******************************************86.57779******* PP

                                 TIGR01536 504 llPeeileR.kKe 515
                                               ++P++i++R kK+
  lcl|NCBI__GCF_000016125.1:WP_011868489.1 462 YVPDYIAQRpKKA 474
                                               *********5555 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (513 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: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.06
# Mc/sec: 4.28
//
[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