Alignments for a candidate for asnB in Methylococcus capsulatus str. Bath

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Methylococcus capsulatus str. Bath

Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate WP_010961366.1 MCA_RS10400 asparagine synthase (glutamine-hydrolyzing)

Query= CharProtDB::CH_005185
         (632 letters)



>NCBI__GCF_000008325.1:WP_010961366.1
          Length = 605

 Score =  271 bits (693), Expect = 6e-77
 Identities = 193/626 (30%), Positives = 297/626 (47%), Gaps = 48/626 (7%)

Query: 1   MCGFVGVFNKHPLAQTADQEELIKQMNQMIVHRGPDSDGYFHDEHVGFGFRRLSIIDVEN 60
           MCG  G+  K    Q     + +  M + + HRGPD  G F +   G    RLSIID+  
Sbjct: 1   MCGIAGLVLKGRNVQA----DRLHPMIERLAHRGPDGQGVFTEGGFGLAHTRLSIIDLSG 56

Query: 61  GGQPLSYEDETYWIIFNGEIYNYIELREELEAKGYTFNTDSDTEVLLATYRHYKEEAASK 120
           G QP+  +D    ++ NGEIYN++ELRE LE +G  F T SD+E +L  Y    E  A +
Sbjct: 57  GRQPILADDGRLAVVANGEIYNHVELREALEREGRRFATHSDSETILHAYALDPEGFAGR 116

Query: 121 LRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTINDQVYFASERKSLM-VAQNDIEIDKE 179
           L GMFAF +++     L   RD  GIKPL+Y  + D++ FASE K+++ +  N   ID  
Sbjct: 117 LHGMFAFALYDGVRRRLVLGRDRLGIKPLFYAALPDRLVFASEMKAILPLLPNAPTIDAG 176

Query: 180 ALQQYMSFQFVPEPSTLDAHVKKVEPGSQFTIRPDGDITFKTYF--------KANFKPVQ 231
           A  Q++         TL + ++++ PG       + ++  + Y+          +F   +
Sbjct: 177 AFSQFLHTHCSTGEETLFSGIRRLGPGEILEADAELNLRKRRYWTPLGVRSRALDFAEAE 236

Query: 232 TEEDKLVKEVRDAIYDSVNVHMRSDVPVGSFLSGGIDSSFIVSVAKEFHPS-LKTFSVGF 290
            E + + ++V       +  H+RSDVP G FLSGG DS+ ++++        ++TFS+G+
Sbjct: 237 AEFEGMFEQV-------MKEHVRSDVPYGLFLSGGNDSAILLAMLSRLQAQPVRTFSIGY 289

Query: 291 EQQGF-SEVDVAKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADPAAIPLYFVA 349
                  E+  A+  A   G  + S  +  E+    +P  VW  DD + D A+ P   ++
Sbjct: 290 VDAAMKDELGDAERIAQVFGSRHTSIRLRREDLFRRIPHTVWAADDLMRDYASFPTSALS 349

Query: 350 KEAKKHVTVALSGEGADELFGGYNIYREPLSLKPFERIPSGLKKMLLHVAAVMPEGMRGK 409
           + A K + V  +GEG DE+FGGY  YR+P            L  +  ++ A    G R +
Sbjct: 350 EAAAKELKVVFTGEGGDEVFGGYRRYRQP-----------RLAWLARNLLAPGTGGFRTR 398

Query: 410 SLLERGCTPLQDRYIGNAKIFEESVKKQLLKHYNPNLSYRDVTKTYFTESSSYSDINKMQ 469
           S   R       R  G A   E        KH+          K +    + +S +   Q
Sbjct: 399 SEWWR---KRSQRLFGPALAAER-------KHFR-----APYLKAWSEAPAVWSHLQHCQ 443

Query: 470 YVDIHTWMRGDILLKADKMTMANSLELRVPFLDKVVFDVASKIPDELKTKNGTTKYLLRK 529
           Y D+ T +   +L+K D+M M   LE RVPFLD  V +    +PD LKT     K  LR+
Sbjct: 444 YTDLVTDLPDSLLVKVDRMMMGFGLEGRVPFLDHRVVEFGLGLPDALKTDGKRPKVFLRR 503

Query: 530 AAEGIVPEHVLNRKKLGFPVPIRHWLKNEMNEWVRNIIQESQTDAYIHKDYVLQLLEDHC 589
            AE  VP+  L  KK GF VP+R WL  E+ + +   +  +              L    
Sbjct: 504 WAERHVPKEHLYTKKRGFTVPVREWLGGELLDRLEGKLSGNAAVREWFDTRHFPALFQAQ 563

Query: 590 ADKADNSRKIWTVLIFMIWHSINIEK 615
             K + SR+I+ ++ F IWH + I++
Sbjct: 564 RKKGNASREIFCLMQFAIWHRLFIDQ 589


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: 917
Number of extensions: 44
Number of successful extensions: 4
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: 632
Length of database: 605
Length adjustment: 37
Effective length of query: 595
Effective length of database: 568
Effective search space:   337960
Effective search space used:   337960
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: 53 (25.0 bits)

Align candidate WP_010961366.1 MCA_RS10400 (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.2836197.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-131  425.9   0.0   1.6e-131  425.7   0.0    1.0  1  NCBI__GCF_000008325.1:WP_010961366.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000008325.1:WP_010961366.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  425.7   0.0  1.6e-131  1.6e-131       1     517 []       2     521 ..       2     521 .. 0.89

  Alignments for each domain:
  == domain 1  score: 425.7 bits;  conditional E-value: 1.6e-131
                             TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsnek.evv 72 
                                           Cgiag+v + ++++   + ++ m+e+lahRGPD++gv+ +    + +l+h RL+iidls+g+QP+ +++ + +
  NCBI__GCF_000008325.1:WP_010961366.1   2 CGIAGLVLKGRNVQ--ADRLHPMIERLAHRGPDGQGVFTE---GGFGLAHTRLSIIDLSGGRQPILADDgRLA 69 
                                           ********977544..489*******************99...8**********************9999*** PP

                             TIGR01536  73 ivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlGi 145
                                           +v nGEIYNh eLre le++G +F t+sD+E iL+ay    e +  rL+GmFAfal+d  +++l+l RDrlGi
  NCBI__GCF_000008325.1:WP_010961366.1  70 VVANGEIYNHVELREALEREGRRFATHSDSETILHAYALDPEGFAGRLHGMFAFALYDGVRRRLVLGRDRLGI 142
                                           **************************************988******************************** PP

                             TIGR01536 146 kPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakal....dgeek 214
                                           kPL+ya   ++l+faSE+Ka+l+l   ++ +d+ a++++l  + ++ e+tlf ++++l p++ l    + + +
  NCBI__GCF_000008325.1:WP_010961366.1 143 KPLFYAALPDRLVFASEMKAILPLLPNAPTIDAGAFSQFLHTHCSTGEETLFSGIRRLGPGEILeadaELNLR 215
                                           *************************99****************99*****************99774333333 PP

                             TIGR01536 215 lee..ywevekee.vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeaksevktFs 284
                                             +  yw     + ++ ++ e+ +e++ ++e+  k+++++dvp+g++lSGG DS ++ a++++  +++v+tFs
  NCBI__GCF_000008325.1:WP_010961366.1 216 --KrrYWTPLGVRsRALDFAEAEAEFEGMFEQVMKEHVRSDVPYGLFLSGGNDSAILLAMLSRLQAQPVRTFS 286
                                           ..3569997665548999******************************************************* PP

                             TIGR01536 285 igfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasiplyllsklarekgvkV 357
                                           ig+ d +  de   a+++a+ +g++h+++ + +e+++  +++ ++a ++++ + as+p+ +ls++a ++ +kV
  NCBI__GCF_000008325.1:WP_010961366.1 287 IGYVDAAMKDELGDAERIAQVFGSRHTSIRLRREDLFRRIPHTVWAADDLMRDYASFPTSALSEAAAKE-LKV 358
                                           ****999999999*****************************************************999.*** PP

                             TIGR01536 358 vLsGeGaDElfgGYeyfreakaeealelpeaselaekklllqaklakeselkellkakleeelkekeelkkel 430
                                           v++GeG+DE+fgGY ++r++  +  ++         +  +   + ++e+  k+ ++   ++  +e+++  + +
  NCBI__GCF_000008325.1:WP_010961366.1 359 VFTGEGGDEVFGGYRRYRQPRLAWLAR------NLLAPGTGGFRTRSEWWRKRSQRLFGPALAAERKHFRAPY 425
                                           *******************85555544......2222222222233333333333333333333333333333 PP

                             TIGR01536 431 kee........seleellrldlelllsdllrak.DrvsmahslEvRvPflDkelvelalsippelklrdgkeK 494
                                            ++        s+l++ ++ dl + l+d l++k Dr++m  +lE RvPflD+++ve+ l +p  lk++ ++ K
  NCBI__GCF_000008325.1:WP_010961366.1 426 LKAwseapavwSHLQHCQYTDLVTDLPDSLLVKvDRMMMGFGLEGRVPFLDHRVVEFGLGLPDALKTDGKRPK 498
                                           33333457888************************************************************** PP

                             TIGR01536 495 vlLreaaeellPeeileRkKeaf 517
                                           v Lr+ ae+++P+e l+ kK++f
  NCBI__GCF_000008325.1:WP_010961366.1 499 VFLRRWAERHVPKEHLYTKKRGF 521
                                           ********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (605 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 34.63
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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