Alignments for a candidate for asnB in Methylocapsa acidiphila B2

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Methylocapsa acidiphila B2

Align Putative asparagine synthetase [glutamine-hydrolyzing]; EC 6.3.5.4 (characterized)
to candidate WP_026606747.1 METAC_RS0108870 asparagine synthase (glutamine-hydrolyzing)

Query= SwissProt::P64248
         (652 letters)



>NCBI__GCF_000427445.1:WP_026606747.1
          Length = 655

 Score =  308 bits (790), Expect = 4e-88
 Identities = 227/668 (33%), Positives = 324/668 (48%), Gaps = 56/668 (8%)

Query: 1   MCGLLAFVAAPAGAAGPEGADAASAIARASHLMRHRGPDESGTWHAVDGASGGVVFGFNR 60
           MCG+  F+ +  G  GP+  +  S + R    + HRGPD  G W   D    G+     R
Sbjct: 1   MCGVAGFLGS--GGVGPD--EWPSLLNRMGAAIAHRGPDSCGIWTDADA---GIGLAHRR 53

Query: 61  LSIIDIAHSHQPLRWGPPEAPD-RYVLVFNGEIYNYLELRDEL-----RTQHGAVFATDG 114
           L+++D++    P    P  +P  R+V++FNGEIYN++ELR EL     +      +    
Sbjct: 54  LAVVDLS----PAGRQPMISPSGRFVIIFNGEIYNHVELRMELDAALEKKSQSIGWRGHS 109

Query: 115 DGEAILAGYHHWGTEV-LQRLRGMFAFALWDTVTRELFCARDPFGIKPLFIATGAGGTAV 173
           D E +LAG+  WG E  L+R  GMFA ALWD   REL  ARD  G KPL+     G    
Sbjct: 110 DTETLLAGFDVWGVETTLKRSVGMFAIALWDKQRRELVLARDRMGEKPLYYGWCNGVFLF 169

Query: 174 ASEKKCLLDLVELVGFDTEIDHRALQHYTVLQYVPEPETLHRGVRRLESGCFARIRADQL 233
            SE K +        F  EID  A+       Y+P P ++++GVR+L+ G   R+ A   
Sbjct: 170 GSELKVIK---AHPAFRGEIDRDAVALLLKHSYIPAPYSIYKGVRKLKPGMLLRVTASSA 226

Query: 234 A---PVITRYF---VPRFAASPITNDNDQARYDEITAVLEDSVAKHMRADVTVGAFLSGG 287
           A   PV+   F        A+P T  + +A  + + A+L  SV+  M ADV +GAFLSGG
Sbjct: 227 AFDDPVVYWSFCEAAESALANPFTGSDSEA-VEALEALLRRSVSNQMLADVPLGAFLSGG 285

Query: 288 IDSTAIAALAIRHNPRLI-TFTTGFEREGFSEIDVAVASAEAIGARHIAKVVSADEFVAA 346
           +DS+ + AL    + + I TFT GF+   ++E   A A A+ +G +H    VS    +  
Sbjct: 286 VDSSTVVALMQAQSSQPIKTFTIGFDESAYNEAKYARAVAKHLGTQHTELYVSPKRAMEV 345

Query: 347 LPEIVWYLDEPVADPALVPLFFVAREARKHVKVVLSGEGADELFGGYTIYREPLSLRPF- 405
           +P +    DEP +D + +P + V++ ARKHV V LSG+  DELFGGYT Y    +L  + 
Sbjct: 346 IPLLPALYDEPFSDSSQIPTYLVSQMARKHVTVSLSGDAGDELFGGYTRYLLARTLWAWA 405

Query: 406 DYLPKPLRRSMGKVSKPLPEGMRGKSLLHRGSLTLEERY----YGN-----ARSFSGAQL 456
             LP P R  +             K +  + S  L +R+    +G+     A  FS    
Sbjct: 406 GKLPGPARCKVASFLSAASPSFWDK-IYEKASHILPQRFRSTHFGHKIHKLAEIFSATSA 464

Query: 457 REVLPGFRPDWTHTDVTAPVYAESAGWDPVA-----------RMQHIDLFTWLRGDILVK 505
            ++  G    W     T     ES     +            RM   D  ++L  DILVK
Sbjct: 465 DDIYDGLISHWRRPTDTVMGATESPSLMSLLKKADSFESFEDRMMAADSLSYLPDDILVK 524

Query: 506 ADKITMANSLELRVPFLDPEVFAVASRLPAGAKITRTTTKYALRRALEPIVPAHVLHRPK 565
            D+  M  SLE RVPFLD  V   A RLP   K+ +  +K+ LR+ L   VP  ++ RPK
Sbjct: 525 VDRAAMGVSLETRVPFLDHRVLEFAWRLPLRMKMRKGESKWILRQVLYKHVPPDLIERPK 584

Query: 566 LGFPVPIRHWLRAGELLEWAYATVGSS---QAGHLVDIAAVYRMLDEHRCGSSDHSRRLW 622
           +GF VPI  WLR G L +WA   +      + G+      + R  DEH+ G  +    LW
Sbjct: 585 MGFGVPIDDWLR-GPLRDWAEGLLNEQRLRREGYFY-AEPIRRKWDEHQSGQHNWQYHLW 642

Query: 623 TMLIFMLW 630
            +L+F  W
Sbjct: 643 DVLMFQAW 650


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: 1079
Number of extensions: 53
Number of successful extensions: 9
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: 655
Length adjustment: 38
Effective length of query: 614
Effective length of database: 617
Effective search space:   378838
Effective search space used:   378838
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_026606747.1 METAC_RS0108870 (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.3758.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.3e-142  461.5   0.0   2.7e-142  461.3   0.0    1.1  1  lcl|NCBI__GCF_000427445.1:WP_026606747.1  METAC_RS0108870 asparagine synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000427445.1:WP_026606747.1  METAC_RS0108870 asparagine synthase (glutamine-hydrolyzing)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  461.3   0.0  2.7e-142  2.7e-142       1     517 []       2     587 ..       2     587 .. 0.87

  Alignments for each domain:
  == domain 1  score: 461.3 bits;  conditional E-value: 2.7e-142
                                 TIGR01536   1 Cgiagivdlkakake.eeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsn 67 
                                               Cg+ag++ +     +   + +++m  ++ahRGPD+ g+w d  +++ +l+hrRLa++dls + +QP+ +
  lcl|NCBI__GCF_000427445.1:WP_026606747.1   2 CGVAGFLGSGGVGPDeWPSLLNRMGAAIAHRGPDSCGIWTD-ADAGIGLAHRRLAVVDLSPAgRQPMIS 69 
                                               999999999887776666899********************.79****************998****** PP

                                 TIGR01536  68 ek.evvivfnGEIYNheeLreelee......kGyeFetksDtEViLaayeewg.eelverLeGmFAfal 128
                                                + + vi+fnGEIYNh eLr el +      + + ++++sDtE +La ++ wg e++++r  GmFA+al
  lcl|NCBI__GCF_000427445.1:WP_026606747.1  70 PSgRFVIIFNGEIYNHVELRMELDAalekksQSIGWRGHSDTETLLAGFDVWGvETTLKRSVGMFAIAL 138
                                               *99*****************9986522222246779********************************* PP

                                 TIGR01536 129 wdekkgelflaRDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlf 197
                                               wd++++el+laRDr+G kPLYy+  +g +lf+SE+K++ a+++++ e+d++a+a ll++++ p + +++
  lcl|NCBI__GCF_000427445.1:WP_026606747.1 139 WDKQRRELVLARDRMGEKPLYYGWCNGVFLFGSELKVIKAHPAFRGEIDRDAVALLLKHSYIPAPYSIY 207
                                               *************************************************************9******* PP

                                 TIGR01536 198 kevkelepakal...dgeeklee...ywevekee.......vkeseeelveelrelledavkkrlvadv 253
                                               k+v++l+p+  l    +++++++   yw+  + +       ++ s++e+ve l+ ll+++v +++ adv
  lcl|NCBI__GCF_000427445.1:WP_026606747.1 208 KGVRKLKPGMLLrvtASSAAFDDpvvYWSFCEAAesalanpFTGSDSEAVEALEALLRRSVSNQMLADV 276
                                               ***********9665444445559999998776668999999*************************** PP

                                 TIGR01536 254 pvgvllSGGlDSslvaaiakkeaksevktFsigfedskdldeskaarkvadelgtehkevliseeevlk 322
                                               p+g++lSGG+DSs+v+a++++++ +++ktF+igf+ +++++e+k+ar+va++lgt+h+e+++s++ +++
  lcl|NCBI__GCF_000427445.1:WP_026606747.1 277 PLGAFLSGGVDSSTVVALMQAQSSQPIKTFTIGFD-ESAYNEAKYARAVAKHLGTQHTELYVSPKRAME 344
                                               ***********************************.99******************************* PP

                                 TIGR01536 323 eleevilaleeptairasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeeale....... 384
                                                ++ +    +ep++++++ip+yl+s++ar++ v+V LsG+ +DElfgGY ++  a    a+        
  lcl|NCBI__GCF_000427445.1:WP_026606747.1 345 VIPLLPALYDEPFSDSSQIPTYLVSQMARKH-VTVSLSGDAGDELFGGYTRYLLARTLWAWAgklpgpa 412
                                               *******************************.**********************999999989999999 PP

                                 TIGR01536 385 .............................lpeaselaekkl.......................llqak 401
                                                                                       +                       +++  
  lcl|NCBI__GCF_000427445.1:WP_026606747.1 413 rckvasflsaaspsfwdkiyekashilpqR----------FrsthfghkihklaeifsatsaddIYD-G 470
                                               999999888888877777766655553330..........133333444444455444444443333.3 PP

                                 TIGR01536 402 lakeselkellkakleeelkekeelkkelkeeseleellrldlelllsdllrak.DrvsmahslEvRvP 469
                                               l ++++    + +  +e+ + ++ lkk+ + es  ++++ +d   +l+d++++k Dr++m  slE RvP
  lcl|NCBI__GCF_000427445.1:WP_026606747.1 471 LISHWRRPTDTVMGATESPSLMSLLKKADSFESFEDRMMAADSLSYLPDDILVKvDRAAMGVSLETRVP 539
                                               33333333333334444444444445555555888999******************************* PP

                                 TIGR01536 470 flDkelvelalsippelklrdgkeKvlLreaaeellPeeileRkKeaf 517
                                               flD++++e+a+++p  +k+r+g+ K++Lr+++ +++P ++ eR+K++f
  lcl|NCBI__GCF_000427445.1:WP_026606747.1 540 FLDHRVLEFAWRLPLRMKMRKGESKWILRQVLYKHVPPDLIERPKMGF 587
                                               **********************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (655 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: 8.42
//
[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