Alignments for a candidate for asnB in Thioalkalivibrio halophilus HL17

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Thioalkalivibrio halophilus HL17

Align Putative asparagine synthetase [glutamine-hydrolyzing] 2; EC 6.3.5.4 (uncharacterized)
to candidate WP_077244558.1 B1A74_RS10125 asparagine synthase (glutamine-hydrolyzing)

Query= curated2:Q58456
         (515 letters)



>NCBI__GCF_001995255.1:WP_077244558.1
          Length = 648

 Score =  228 bits (580), Expect = 7e-64
 Identities = 154/426 (36%), Positives = 226/426 (53%), Gaps = 39/426 (9%)

Query: 1   MCGINGIIRFGKEVIKEEINKMNKAIKHRGPDDEGIFIYNFKNYSIGLGHVRLAILDLSE 60
           MCGI G        + +  ++M   I  RGPDD G++          L H RL+I+DLS 
Sbjct: 1   MCGIVGYWSRNSRSV-DVASRMAHRIATRGPDDAGVWAEG--EGEPVLAHRRLSIVDLSP 57

Query: 61  KGHQPMGYNVDEDKIIYRDDELDRADIIIVYNGEIYNYLELKEKFNLETETG-------T 113
            GHQPM                     ++ YNGEIYN+ EL+++  LE E G       +
Sbjct: 58  AGHQPMVSPCGR--------------YVLSYNGEIYNHTELRQE--LEREGGGFDWRGHS 101

Query: 114 DTEVILKLYNKLGFD-CVKEFNGMWAFCIFDKKKGLIFCSRDRLGVKPFYYYWDGNEFIF 172
           DTE +L      G    ++  NGM+AF ++D+ +  +F +RDR+G KP YY   G+ F+F
Sbjct: 102 DTETLLAALRYWGVHGALERLNGMFAFALWDRTERTLFLARDRMGEKPLYYGRSGDTFLF 161

Query: 173 SSELKGILAVKEINKKENINKDAVELYFALGFIPSPYSIYKNTFKLEARQNLIFDLDKRE 232
            SELK + A  +   +  +++DA+ L      +P+P+SIY+  +KL     L+      +
Sbjct: 162 GSELKALAAHPDW--RGEVDRDALALMLRYNNVPAPWSIYRGIYKLPPAHYLVVRGQGHQ 219

Query: 233 IRK-YYYWELPDY------KPIYDKKKLIEEGKKLLYDAVKIRMRSDVPVGAFLSGGLDS 285
           + +   YW+LP+       +   +   L +E  +LL D+V  RM +DVP+GAFLSGG DS
Sbjct: 220 VGEPECYWDLPEVASEGAREAKGEPDALADELDELLRDSVGRRMMADVPLGAFLSGGFDS 279

Query: 286 STVVGVMREFTDLSKLHTFSIG-FEGKYDETPYIKIVVDYFKTQHHHYYFKERDFEELID 344
           + VV  M+       + TFSIG  + +YDE  +   V  +  T H   Y    D + +I 
Sbjct: 280 TMVVAQMQA-QSARPVKTFSIGNADAEYDEAHHAAAVARHLGTDHRELYVTPEDAQAVIP 338

Query: 345 KYSWIYDEPFGDYSGFPTYKVSEMARKFVTVVLSGDGGDEVFGGYMTHLNGYRM-DFIRK 403
           +   I+DEPF D S  PTY VSE+AR+ VTV LSGDGGDE+ GGY  H+ G  +   + +
Sbjct: 339 RLPEIFDEPFADSSQIPTYLVSELARRDVTVTLSGDGGDELLGGYNRHVVGPGVWRRVNR 398

Query: 404 LPKFLR 409
           LP +LR
Sbjct: 399 LPGWLR 404


Lambda     K      H
   0.322    0.144    0.434 

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: 800
Number of extensions: 37
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 515
Length of database: 648
Length adjustment: 36
Effective length of query: 479
Effective length of database: 612
Effective search space:   293148
Effective search space used:   293148
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 (21.9 bits)
S2: 53 (25.0 bits)

Align candidate WP_077244558.1 B1A74_RS10125 (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.3293292.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.7e-153  496.1   0.0     1e-152  495.7   0.0    1.2  1  NCBI__GCF_001995255.1:WP_077244558.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001995255.1:WP_077244558.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  495.7   0.0    1e-152    1e-152       1     517 []       2     574 ..       2     574 .. 0.89

  Alignments for each domain:
  == domain 1  score: 495.7 bits;  conditional E-value: 1e-152
                             TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsnek.ev 71 
                                           Cgi+g   ++     + + +++m++++a RGPD+ gvw +  e + +l+hrRL+i+dls + +QP+ +   ++
  NCBI__GCF_001995255.1:WP_077244558.1   2 CGIVGYWSRNSR---SVDVASRMAHRIATRGPDDAGVWAE-GEGEPVLAHRRLSIVDLSPAgHQPMVSPCgRY 70 
                                           *****9999665...55789********************.899***************998******999** PP

                             TIGR01536  72 vivfnGEIYNheeLreeleekG..yeFetksDtEViLaayeewg.eelverLeGmFAfalwdekkgelflaRD 141
                                           v+ +nGEIYNh eLr+ele++G  ++++++sDtE +Laa+++wg + ++erL+GmFAfalwd+ +++lflaRD
  NCBI__GCF_001995255.1:WP_077244558.1  71 VLSYNGEIYNHTELRQELEREGggFDWRGHSDTETLLAALRYWGvHGALERLNGMFAFALWDRTERTLFLARD 143
                                           ******************9985338889****************999************************** PP

                             TIGR01536 142 rlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakal..... 209
                                           r+G kPLYy++ ++++lf+SE+Kal a+++ + e+d++ala +l +++vp + ++++++++l+pa++l     
  NCBI__GCF_001995255.1:WP_077244558.1 144 RMGEKPLYYGRSGDTFLFGSELKALAAHPDWRGEVDRDALALMLRYNNVPAPWSIYRGIYKLPPAHYLvvrgq 216
                                           ********************************************************************99763 PP

                             TIGR01536 210 .dgeeklee..ywevekee......vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiak 273
                                            ++  +     yw++ + +       k + ++l +el+ell+d+v +r++advp+g++lSGG DS++v+a ++
  NCBI__GCF_001995255.1:WP_077244558.1 217 gHQVGE--PecYWDLPEVAsegareAKGEPDALADELDELLRDSVGRRMMADVPLGAFLSGGFDSTMVVAQMQ 287
                                           333333..266***99888888988889999****************************************** PP

                             TIGR01536 274 keaksevktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasiplyll 346
                                           ++++++vktFsig + ++++de+++a++va++lgt+h+e+++++e++ + ++++  +++ep+a++++ip+yl+
  NCBI__GCF_001995255.1:WP_077244558.1 288 AQSARPVKTFSIGNA-DAEYDEAHHAAAVARHLGTDHRELYVTPEDAQAVIPRLPEIFDEPFADSSQIPTYLV 359
                                           ***************.9******************************************************** PP

                             TIGR01536 347 sklarekgvkVvLsGeGaDElfgGYeyfreakaeeale...............................lpea 388
                                           s+lar++ v+V LsG+G+DEl+gGY+++   +    ++                               lp  
  NCBI__GCF_001995255.1:WP_077244558.1 360 SELARRD-VTVTLSGDGGDELLGGYNRHVVGPG--VWRrvnrlpgwlrgflggavgnlsqrdlrqwrrrLPAR 429
                                           *******.*******************987543..33333489999999999999988888876666663333 PP

                             TIGR01536 389 selaekkl....................llqaklakeselkellkakleeelkekeelkkelkeeseleellr 441
                                           ++     +                      ++ l+++++  e +    +e++++   ++  +      e+++ 
  NCBI__GCF_001995255.1:WP_077244558.1 430 MQ-----VpnlelkleklakalgasdgpGFYRALRSRWKAPEGMVLGASEQQEQEGPVDWLSDLPGLREQMML 497
                                           33.....033333444555666777777555667777776666666666666666666666666699****** PP

                             TIGR01536 442 ldlelllsdllrak.DrvsmahslEvRvPflDkelvelalsippelklrdgkeKvlLreaaeellPeeileRk 513
                                           ld+ ++l+d+++ k Dr+sma slE+RvP+lD++lve+a+++p+e+k+rdg+ K+lLr+++++++P++++eR+
  NCBI__GCF_001995255.1:WP_077244558.1 498 LDMLTYLPDDILTKvDRASMAVSLEARVPLLDHRLVEFAWQVPTEYKVRDGQGKWLLRKVLDRYVPSSLMERP 570
                                           ************************************************************************* PP

                             TIGR01536 514 Keaf 517
                                           K++f
  NCBI__GCF_001995255.1:WP_077244558.1 571 KQGF 574
                                           **99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (648 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: 38.46
//
[ok]

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