Alignments for a candidate for asnB in Sedimenticola selenatireducens DSM 17993

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Sedimenticola selenatireducens DSM 17993

Align asparagine synthase (glutamine-hydrolysing) 3; EC 6.3.5.4 (characterized)
to candidate WP_029132074.1 A3GO_RS0102565 N-acetylglutaminylglutamine amidotransferase

Query= CharProtDB::CH_007942
         (614 letters)



>NCBI__GCF_000428045.1:WP_029132074.1
          Length = 593

 Score =  258 bits (658), Expect = 7e-73
 Identities = 171/540 (31%), Positives = 274/540 (50%), Gaps = 25/540 (4%)

Query: 1   MCGITGWVDFKKQLVQEKQTMDRMTDTLSKRGPDDSNVWGEHHVLFGHKRLAVVDI-EGG 59
           MCGI G +        +   + RMT  L +RGPD    + +  + FGH+RLA++D+ E  
Sbjct: 1   MCGICGELRLDGGR-PDLGAISRMTARLDRRGPDHEGSYSDGPLAFGHRRLAIIDLSERA 59

Query: 60  RQPMACTYKGDTYTIIYNGELYNTEDLRKELRARGHQFERTSDTEVLLHSYIEWQEDCVD 119
            QPM     G    +++NG +YN   LR+ L+ +G+ F    D+EV+L ++  W + CV+
Sbjct: 60  NQPMVDQELG--LALVFNGTIYNYPALRETLKQKGYHFYSDGDSEVILKAWHAWGDRCVE 117

Query: 120 HLNGIFAFAVWDEKRNLLFAARDRLGVKPFFYTKEGSSFLFGSEIKAILAHPDIKARVDR 179
            L G+FAFA+WD+ +  LF ARDR+G+KPF+Y+   S F F S ++A+LA   +   +D 
Sbjct: 118 QLQGMFAFAIWDQGKKQLFMARDRMGIKPFYYSHSDSQFRFASNVQALLASGGVDISLDA 177

Query: 180 TGLSEIFGLGPSRTPGTGIFKGIKEIRPAHALTFSKDGLNI-WRYWNVESEK--HTDSFD 236
             L   F L         I +G++++ P H+L    DG     RYW + + +     S  
Sbjct: 178 VALHNQFTLHAVVPAPRTILQGVRKLAPGHSLLLDADGKRTERRYWQLSATRPARPRSDG 237

Query: 237 DTVANVRSLFQDAV-TRQLVSDVPVCTFLSGGLDSSAITAIAAGHFEKEGKAPLHTYSID 295
           + + ++    + AV  R  +SDVPV   LSGGLDSS + A+ A    + G + L T+S+ 
Sbjct: 238 EWLESIHDALRLAVHKRNNISDVPVGVLLSGGLDSSLLVALLA----ESGVSDLRTFSVG 293

Query: 296 YEENDKYFQASAFQPNDDGPWIEKMTEAFGTTHHKCVISQKDLVDHLEEAVLVKDLPGMA 355
           +E++    + S F+ +D      ++ E +GTTHHK +I  ++++  L EAV     P   
Sbjct: 294 FEDHPDE-KGSEFEYSD------QVVERYGTTHHKYLIPNEEVLKRLPEAVDAMAEPMFG 346

Query: 356 DVDSSLLWFCREIKKDFVVSLSGECADEIFGGYPWFHTADVE-SGFPWMRSTEERIKLLS 414
               +      ++ K   V  SG+ ADE+FGGY W+     E  G P  R          
Sbjct: 347 QDAVAFYLLSEQVSKQIKVVQSGQGADEVFGGYFWYSRMMAEQQGSPVERFARHYFDRDH 406

Query: 415 DSWQKKLNLKEYVNAKYEETLAETPLLDGETGVDKARRQLFYLNMLWFMT-NLLDRKDRM 473
           + + + +  +   +    + +AE   L GE G D     +  +++   +  + + R D M
Sbjct: 407 EEYLRMVTAEYRGDDYTSQHIAE---LLGEPGADSFMDAVLRMDVTTLIVDDPVKRVDNM 463

Query: 474 SMGASLEVRVPFADHRLVEYVWNIPWEMKMHDNREKGILRKALEGILPDDILYRKKSPYP 533
           +M   LE RVPF D +LVE     P E+K+ +   K  L+    GILPD ++ R K  +P
Sbjct: 464 TMAWGLEARVPFLDQQLVELAAQCPPELKLREG-GKYPLKAMARGILPDSVIDRPKGYFP 522


Lambda     K      H
   0.320    0.137    0.425 

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: 904
Number of extensions: 31
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: 614
Length of database: 593
Length adjustment: 37
Effective length of query: 577
Effective length of database: 556
Effective search space:   320812
Effective search space used:   320812
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 (21.8 bits)
S2: 53 (25.0 bits)

Align candidate WP_029132074.1 A3GO_RS0102565 (N-acetylglutaminylglutamine amidotransferase)
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.8648.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.8e-141  456.9   0.0   6.6e-141  456.7   0.0    1.0  1  lcl|NCBI__GCF_000428045.1:WP_029132074.1  A3GO_RS0102565 N-acetylglutaminy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000428045.1:WP_029132074.1  A3GO_RS0102565 N-acetylglutaminylglutamine amidotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  456.7   0.0  6.6e-141  6.6e-141       1     516 [.       2     520 ..       2     521 .. 0.90

  Alignments for each domain:
  == domain 1  score: 456.7 bits;  conditional E-value: 6.6e-141
                                 TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsne 68 
                                               Cgi g + l+   + +  ai++m+ +l +RGPD+eg ++d      ++ghrRLaiidlse  +QP+ ++
  lcl|NCBI__GCF_000428045.1:WP_029132074.1   2 CGICGELRLDGG-RPDLGAISRMTARLDRRGPDHEGSYSD---GPLAFGHRRLAIIDLSERaNQPMVDQ 66 
                                               999999999775.44689*******************999...8***************999******* PP

                                 TIGR01536  69 k.evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgel 136
                                               +   ++vfnG IYN+ +Lre+l++kGy+F ++ D+EViL+a+++wg ++ve+L+GmFAfa+wd+ k++l
  lcl|NCBI__GCF_000428045.1:WP_029132074.1  67 ElGLALVFNGTIYNYPALRETLKQKGYHFYSDGDSEVILKAWHAWGDRCVEQLQGMFAFAIWDQGKKQL 135
                                               **99***************************************************************** PP

                                 TIGR01536 137 flaRDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlq.lvptektlfkevkele 204
                                               f+aRDr+GikP+Yy+  ++++ faS ++alla   ++ +ld+ al++++tl+ +vp ++t+ ++v++l 
  lcl|NCBI__GCF_000428045.1:WP_029132074.1 136 FMARDRMGIKPFYYSHSDSQFRFASNVQALLASGGVDISLDAVALHNQFTLHaVVPAPRTILQGVRKLA 204
                                               ****************************************************999************** PP

                                 TIGR01536 205 pakal....dgeekleeywevekee..vkeseeelveelrelledavkkrlv.advpvgvllSGGlDSs 266
                                               p+++l    dg+++ ++yw+++ ++  +  s+ e  e++ ++l+ av+kr   +dvpvgvllSGGlDSs
  lcl|NCBI__GCF_000428045.1:WP_029132074.1 205 PGHSLlldaDGKRTERRYWQLSATRpaRPRSDGEWLESIHDALRLAVHKRNNiSDVPVGVLLSGGLDSS 273
                                               *****998777777777***99988667788999**************99766**************** PP

                                 TIGR01536 267 lvaaiakkeaksevktFsigfedskdldesk..aarkvadelgtehkevliseeevlkeleevilalee 333
                                               l++a++++   s+++tFs+gfed++d + s+  +  +v++  gt+h+++li +eevlk l+e + a+ e
  lcl|NCBI__GCF_000428045.1:WP_029132074.1 274 LLVALLAESGVSDLRTFSVGFEDHPDEKGSEfeYSDQVVERYGTTHHKYLIPNEEVLKRLPEAVDAMAE 342
                                               ******999999**********8877765554499********************************** PP

                                 TIGR01536 334 ptairasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeealelpeaselaekklllqakl 402
                                               p+  ++++  ylls++++++ +kVv sG+GaDE+fgGY ++ ++ ae++   p  +++  +++  +   
  lcl|NCBI__GCF_000428045.1:WP_029132074.1 343 PMFGQDAVAFYLLSEQVSKQ-IKVVQSGQGADEVFGGYFWYSRMMAEQQGS-PV-ERF--ARHYFD--- 403
                                               ********************.**********************98888775.22.221..222222... PP

                                 TIGR01536 403 akeselkellkakleeelkekeelkkelkee...seleellrldlelllsdl.lrakDrvsmahslEvR 467
                                               +++ e  +++ a+++ +  ++++ ++ l e    s ++++lr d+++l+ d+ +++ D ++ma++lE+R
  lcl|NCBI__GCF_000428045.1:WP_029132074.1 404 RDHEEYLRMVTAEYRGDDYTSQHIAELLGEPgadSFMDAVLRMDVTTLIVDDpVKRVDNMTMAWGLEAR 472
                                               23444556666666666655555555555545559*********9998776626666************ PP

                                 TIGR01536 468 vPflDkelvelalsippelklrdgkeKvlLreaaeellPeeileRkKea 516
                                               vPflD++lvela++ ppelklr+g  K+ L+ +a+++lP+++ +R+K  
  lcl|NCBI__GCF_000428045.1:WP_029132074.1 473 VPFLDQQLVELAAQCPPELKLREG-GKYPLKAMARGILPDSVIDRPKGY 520
                                               *********************987.7********************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (593 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: 00:00:00.02
# Mc/sec: 10.83
//
[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