Alignments for a candidate for asnB in Methylocystis bryophila S285

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Methylocystis bryophila S285

Align Putative asparagine synthetase [glutamine-hydrolyzing]; EC 6.3.5.4 (characterized)
to candidate WP_085769993.1 B1812_RS01355 asparagine synthase (glutamine-hydrolyzing)

Query= SwissProt::P64248
         (652 letters)



>NCBI__GCF_002117405.1:WP_085769993.1
          Length = 670

 Score =  290 bits (742), Expect = 1e-82
 Identities = 231/669 (34%), Positives = 321/669 (47%), Gaps = 61/669 (9%)

Query: 1   MCGLLAFVAAPAGAAGPEGADAASAIARASHLMRHRGPDESGTWHAVDGASGGVVFGFNR 60
           MCG+ A + +   ++G        A+ +A +L   RGPD   T+   +    GV  G  R
Sbjct: 1   MCGI-AGILSDLYSSGARLEAPIGAMTKALYL---RGPDAGATFVEPEA---GVALGHRR 53

Query: 61  LSIIDIAH-SHQPLRWGPPEAPDRYVLVFNGEIYNYLELRDELRTQHGAVFATDGDGEAI 119
           L+I+D++    QP+R     A  RYV+VFNGEIYN+L+LR EL  +   ++    D E +
Sbjct: 54  LAILDLSERGAQPMR----SACGRYVIVFNGEIYNHLDLRRELGARREVMWRGTSDTETL 109

Query: 120 LAGYHHWG-TEVLQRLRGMFAFALWDTVTRELFCARDPFGIKPL---FIATGAGGTAV-A 174
           L  +  +G  E L++  GMFA  LWD   R L  ARD FG KPL   FI  G     V  
Sbjct: 110 LECFVEFGIAETLKKSVGMFALGLWDRRDRRLILARDRFGEKPLYYGFIGRGKEKAFVFG 169

Query: 175 SEKKCLLDLVELVGFDTEIDHRALQHYTVLQYVPEPETLHRGVRRLESGCFARIRADQLA 234
           SE K L        F   ID  A+  +    YVP P +++  + +LE G    + A+ ++
Sbjct: 170 SELKALR---AHPAFSNPIDSVAVNLFLQYCYVPAPRSIYEDIFKLEPGTTLTLNAEDVS 226

Query: 235 PV---ITRYF-----VPRFAASPITNDNDQARYDEITAVLEDSVAKHMRADVTVGAFLSG 286
                + RY+     +    A+P+ ++ +    + + A L D+VA  + ADV VGAFLSG
Sbjct: 227 TGRRRVERYWDYQAVILAGLAAPLLDEREAL--ERLEAALSDAVALQLVADVPVGAFLSG 284

Query: 287 GIDSTAIAALAIRHNPRLI-TFTTGFEREGFSEIDVAVASAEAIGARHIAKVVSADEFVA 345
           GIDS+ I AL    + R   TFT GF+  GF E   A   A  +   H    V+ +E  A
Sbjct: 285 GIDSSTIVALMQARSSRPTQTFTIGFDEAGFDESPHAREVARHLQTDHHEIRVTPEETRA 344

Query: 346 ALPEIVWYLDEPVADPALVPLFFVAREARKHVKVVLSGEGADELFGGYTIYREPLSL-RP 404
            +P +    DEP AD + +P   V   AR+ V V LSG+  DEL GGY  Y    SL R 
Sbjct: 345 IVPRLPETYDEPFADSSQIPTSIVCAVARRSVTVALSGDAGDELLGGYNRYVLGPSLWRR 404

Query: 405 FDYLPKPLRRSMGKVSKPLPE----------GMRGKSLLHRGSLTLEERYYGNARSFSGA 454
             + P PLR  +G V   LP           G+ GK    R          G+ RS    
Sbjct: 405 LAFAPAPLRAVLGGVMAQLPSAAWDVAMRMPGLGGKLAPFRDKAYKLAPVLGSMRSAD-- 462

Query: 455 QLREVLPGFRPDWTHTDVTA------PVYAESAGWDP-----VARMQHIDLFTWLRGDIL 503
              ++      +W   D  A          E+   DP       RM   D  T+L  DIL
Sbjct: 463 ---DMYRALATEWREQDAPALGASDMATRFENPSLDPRIRAPAERMMAFDALTYLPDDIL 519

Query: 504 VKADKITMANSLELRVPFLDPEVFAVASRLPAGAKITRTTTKYALRRALEPIVPAHVLHR 563
            K D+  M+ SLE RVP LD  +  +A RLP   KI     K+ALR+ L   VP  ++ R
Sbjct: 520 TKVDRAAMSVSLETRVPLLDHRIAELAWRLPLSMKIRDGVGKWALRQILYKHVPRELVER 579

Query: 564 PKLGFPVPIRHWLRAGELLEWAYATVG--SSQAGHLVDIAAVYRMLDEHRCGSSDHSRRL 621
           PK GF +PI  WLR G L +WA   +   + +AG  + + AV R+  EHR G  + + RL
Sbjct: 580 PKAGFAIPIGAWLR-GPLRDWADELLSEPALRAGGHLQVEAVRRLWLEHRSGQRNWTMRL 638

Query: 622 WTMLIFMLW 630
           W +L+F  W
Sbjct: 639 WNLLMFQAW 647


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: 1104
Number of extensions: 67
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: 652
Length of database: 670
Length adjustment: 38
Effective length of query: 614
Effective length of database: 632
Effective search space:   388048
Effective search space used:   388048
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_085769993.1 B1812_RS01355 (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.26464.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-133  432.7   0.0   1.5e-133  432.5   0.0    1.1  1  lcl|NCBI__GCF_002117405.1:WP_085769993.1  B1812_RS01355 asparagine synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002117405.1:WP_085769993.1  B1812_RS01355 asparagine synthase (glutamine-hydrolyzing)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  432.5   0.0  1.5e-133  1.5e-133       1     517 []       2     584 ..       2     584 .. 0.88

  Alignments for each domain:
  == domain 1  score: 432.5 bits;  conditional E-value: 1.5e-133
                                 TIGR01536   1 Cgiagivdlkakake.eeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsn 67 
                                               Cgiagi+ +   +    e+ i +m+++l  RGPDa +++ + +e++++lghrRLai dlse  aQP+++
  lcl|NCBI__GCF_002117405.1:WP_085769993.1   2 CGIAGILSDLYSSGArLEAPIGAMTKALYLRGPDAGATFVE-PEAGVALGHRRLAILDLSERgAQPMRS 69 
                                               ******99876666666789*********************.9*****************988****** PP

                                 TIGR01536  68 ek.evvivfnGEIYNheeLreeleek.GyeFetksDtEViLaayeewg.eelverLeGmFAfalwdekk 133
                                               +  ++vivfnGEIYNh +Lr+el ++    ++++sDtE +L+ + e+g  e++++  GmFA+ lwd+++
  lcl|NCBI__GCF_002117405.1:WP_085769993.1  70 ACgRYVIVFNGEIYNHLDLRRELGARrEVMWRGTSDTETLLECFVEFGiAETLKKSVGMFALGLWDRRD 138
                                               *9*********************986256799************************************* PP

                                 TIGR01536 134 gelflaRDrlGikPLYyase....qgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfk 198
                                               ++l+laRDr+G kPLYy+      +++++f+SE+Kal a++++ + +d  a+  +l++ +vp ++++++
  lcl|NCBI__GCF_002117405.1:WP_085769993.1 139 RRLILARDRFGEKPLYYGFIgrgkEKAFVFGSELKALRAHPAFSNPIDSVAVNLFLQYCYVPAPRSIYE 207
                                               *****************9654344788****************************************** PP

                                 TIGR01536 199 evkelepakal........dgeekleeywevekee......vkeseeelveelrelledavkkrlvadv 253
                                               ++++lep+  l        +g +++e+yw+ +            +e+e+ e+l+ +l dav+ +lvadv
  lcl|NCBI__GCF_002117405.1:WP_085769993.1 208 DIFKLEPGTTLtlnaedvsTGRRRVERYWDYQAVIlaglaaPLLDEREALERLEAALSDAVALQLVADV 276
                                               **********99999987777777788****99988898877778999********************* PP

                                 TIGR01536 254 pvgvllSGGlDSslvaaiakkeaksevktFsigfedskdldeskaarkvadelgtehkevliseeevlk 322
                                               pvg++lSGG+DSs+++a++++ + ++ +tF+igf+ ++ +des +ar+va++l t+h+e+ +++ee  +
  lcl|NCBI__GCF_002117405.1:WP_085769993.1 277 PVGAFLSGGIDSSTIVALMQARSSRPTQTFTIGFD-EAGFDESPHAREVARHLQTDHHEIRVTPEETRA 344
                                               ***********************************.********************************* PP

                                 TIGR01536 323 eleevilaleeptairasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeeale....... 384
                                                ++++  + +ep+a++++ip+ +++  ar+  v+V+LsG+ +DEl+gGY+++   ++    +       
  lcl|NCBI__GCF_002117405.1:WP_085769993.1 345 IVPRLPETYDEPFADSSQIPTSIVCAVARRS-VTVALSGDAGDELLGGYNRYVLGPSLW--Rrlafapa 410
                                               ******************************9.********************9876543..33358899 PP

                                 TIGR01536 385 ..............................lpeaselaekkl....................llqakla 403
                                                                             l                                +++ la
  lcl|NCBI__GCF_002117405.1:WP_085769993.1 411 plravlggvmaqlpsaawdvamrmpglggkL----------ApfrdkayklapvlgsmrsadDMYRALA 469
                                               9999988887776666655555544444441..........0444444555566444443333445555 PP

                                 TIGR01536 404 keselkellkakleeelkekeelkkelkeeseleellrldlelllsdllrak.DrvsmahslEvRvPfl 471
                                               +e++++       ++  +++e+ + +   +   e+++  d+ ++l+d+++ k Dr++m  slE RvP+l
  lcl|NCBI__GCF_002117405.1:WP_085769993.1 470 TEWREQDAPALGASDMATRFENPSLDPRIRAPAERMMAFDALTYLPDDILTKvDRAAMSVSLETRVPLL 538
                                               55555555555555555555555555555599************************************* PP

                                 TIGR01536 472 DkelvelalsippelklrdgkeKvlLreaaeellPeeileRkKeaf 517
                                               D++++ela+++p ++k+rdg  K+ Lr+++ +++P+e++eR+K++f
  lcl|NCBI__GCF_002117405.1:WP_085769993.1 539 DHRIAELAWRLPLSMKIRDGVGKWALRQILYKHVPRELVERPKAGF 584
                                               ********************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (670 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: 00:00:00.03
# Mc/sec: 10.73
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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