Alignments for a candidate for asnB in Prosthecochloris aestuarii DSM 271

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Prosthecochloris aestuarii DSM 271

Align asparagine synthase (glutamine-hydrolysing) 3; EC 6.3.5.4 (characterized)
to candidate WP_012504711.1 PAES_RS00550 N-acetylglutaminylglutamine amidotransferase

Query= CharProtDB::CH_007942
         (614 letters)



>NCBI__GCF_000020625.1:WP_012504711.1
          Length = 592

 Score =  256 bits (653), Expect = 3e-72
 Identities = 176/587 (29%), Positives = 282/587 (48%), Gaps = 40/587 (6%)

Query: 1   MCGITGWVDFKKQLVQEKQTMDRMTDTLSKRGPDDSNVWGEHHVLFGHKRLAVVDIEG-G 59
           MCGI G + F         T+D M   L  RGPD   V+  + + FGH+RL ++D+    
Sbjct: 1   MCGIAGELRFDSAAASST-TVDAMLGILEPRGPDAQGVFAHNRICFGHRRLKIIDLSDCA 59

Query: 60  RQPMACTYKGDTYTIIYNGELYNTEDLRKELRARGHQFERTSDTEVLLHSYIEWQEDCVD 119
            QPM  +  G    +++NG +YN  +L  EL  +G+ F   SDTE+++ +Y  W EDCV 
Sbjct: 60  SQPMVDSALG--LVLVFNGAVYNYRELCTELVGKGYSFFSQSDTEIIIKAYHAWGEDCVG 117

Query: 120 HLNGIFAFAVWDEKRNLLFAARDRLGVKPFFYTKEGSSFLFGSEIKAILAHPDIKARVDR 179
           HL G+FAFA+W+      F ARDRLG+KP ++T++ +S  F S + A+L    +   +D 
Sbjct: 118 HLQGMFAFAIWERDTGRTFFARDRLGIKPLYFTEDNASMRFASSLPALLKSGAVDTAIDP 177

Query: 180 TGLSEIFGLGPSRTPGTGIFKGIKEIRPAHALTFSKDGLNIWR-YWNVE----SEKHTDS 234
             L               IF+GI+++ PA  +    DG    R YW  +     E+   S
Sbjct: 178 AALDCYMSFHSVVPAPWTIFRGIRKLPPATTMMVEPDGRKQQRTYWQPDYSRSDEERRRS 237

Query: 235 FDDTVANVRSLFQDAVTRQLVSDVPVCTFLSGGLDSSAITAIAAGHFEKEGKAPLHTYSI 294
             + +  V    + AV R+LV+DVPV   LSGGLDSS +  + +   ++     L T+S+
Sbjct: 238 AGEWIDAVHDALKLAVQRRLVADVPVGVLLSGGLDSSLVVGLLSELVQRH----LSTFSV 293

Query: 295 DYEENDKYFQASAFQPNDDGPWIEKMTEAFGTTHHKCVISQKDLVDHLEEAVLVKDLPGM 354
            +E+        A +  ++  + + + E + T HHK  +  ++L  HL + V     P +
Sbjct: 294 GFED-------VAEEEGNEFRYSDIIAERYSTDHHKIFVDHRELQTHLSDCVRAMSEPMV 346

Query: 355 ADVDSSLLWFCREIKKDFVVSLSGECADEIFGGYPWF----HTADVE-----SGFPWMRS 405
           +          RE+ +   V  SG+ ADE+F GY W+    +T   E     SG  + R 
Sbjct: 347 SHDVIGFYLLSREVSQHVRVVQSGQGADEVFAGYHWYPPMMNTPPTEAYSTYSGVFFDRD 406

Query: 406 TEERIKLLSDSWQKKLNLKEYVNAKYEETLAETPLLDGETGVDKARRQLFYLNMLWFMTN 465
             E  + ++ S+  + +   +V   +    AE P       +DKA R     + +  + +
Sbjct: 407 FNEYRQAVNSSFITEDHAAAFVRNHFAMPGAEEP-------IDKALR---LDSTIMLVDD 456

Query: 466 LLDRKDRMSMGASLEVRVPFADHRLVEYVWNIPWEMKMHDNREKGILRKALEGILPDDIL 525
            + R D M+M   LE RVPF DH LVE    IP E K+ D   K +L++    I+P +++
Sbjct: 457 PVKRVDNMTMAWGLEARVPFLDHELVELAAKIPAEYKVKDG-GKYVLKEVGRRIIPHEVI 515

Query: 526 YRKKSPYPKTHHPEYTKGVSEWLKTIRSQKDSVLHTLLDRKQLDQLL 572
            R K  +P            +  K I +Q  +    + +R+ +D LL
Sbjct: 516 DRPKGYFPVPALKYLEGEYLDMAKNILNQDAAKQRKIFNREYVDMLL 562


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: 860
Number of extensions: 34
Number of successful extensions: 6
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: 592
Length adjustment: 37
Effective length of query: 577
Effective length of database: 555
Effective search space:   320235
Effective search space used:   320235
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_012504711.1 PAES_RS00550 (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.18766.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.7e-139  450.3   0.0   6.6e-139  450.1   0.0    1.0  1  lcl|NCBI__GCF_000020625.1:WP_012504711.1  PAES_RS00550 N-acetylglutaminylg


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020625.1:WP_012504711.1  PAES_RS00550 N-acetylglutaminylglutamine amidotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  450.1   0.0  6.6e-139  6.6e-139       1     516 [.       2     521 ..       2     522 .. 0.94

  Alignments for each domain:
  == domain 1  score: 450.1 bits;  conditional E-value: 6.6e-139
                                 TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsne 68 
                                               Cgiag +  + +a++ + ++++ml  l+ RGPDa+gv+ +   ++ ++ghrRL iidls+   QP+ + 
  lcl|NCBI__GCF_000020625.1:WP_012504711.1   2 CGIAGELRFDSAAAS-STTVDAMLGILEPRGPDAQGVFAH---NRICFGHRRLKIIDLSDCaSQPMVDS 66 
                                               *********998777.59**********************...7****************99******* PP

                                 TIGR01536  69 k.evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgel 136
                                               +   v+vfnG +YN++eL  el  kGy+F ++sDtE+i++ay++wge++v +L+GmFAfa+w++ +g+ 
  lcl|NCBI__GCF_000020625.1:WP_012504711.1  67 AlGLVLVFNGAVYNYRELCTELVGKGYSFFSQSDTEIIIKAYHAWGEDCVGHLQGMFAFAIWERDTGRT 135
                                               **9****************************************************************** PP

                                 TIGR01536 137 flaRDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlq.lvptektlfkevkele 204
                                               f aRDrlGikPLY+++++ ++ faS + all+  ++++++d +al  +++++ +vp + t+f+++++l+
  lcl|NCBI__GCF_000020625.1:WP_012504711.1 136 FFARDRLGIKPLYFTEDNASMRFASSLPALLKSGAVDTAIDPAALDCYMSFHsVVPAPWTIFRGIRKLP 204
                                               ****************************************************9999************* PP

                                 TIGR01536 205 pakal....dgeekleeywevekee....vkeseeelveelrelledavkkrlvadvpvgvllSGGlDS 265
                                               pa  +    dg ++ ++yw+ ++++    ++ s  e ++ + ++l+ av++rlvadvpvgvllSGGlDS
  lcl|NCBI__GCF_000020625.1:WP_012504711.1 205 PATTMmvepDGRKQQRTYWQPDYSRsdeeRRRSAGEWIDAVHDALKLAVQRRLVADVPVGVLLSGGLDS 273
                                               ****9997766666777***99988666788888999******************************** PP

                                 TIGR01536 266 slvaaiakkeaksevktFsigfe..dskdldeskaarkvadelgtehkevliseeevlkeleevilale 332
                                               slv+ ++++ +++++ tFs+gfe   +++ +e ++   +a+   t+h+++ +++ e+  +l + ++a+ 
  lcl|NCBI__GCF_000020625.1:WP_012504711.1 274 SLVVGLLSELVQRHLSTFSVGFEdvAEEEGNEFRYSDIIAERYSTDHHKIFVDHRELQTHLSDCVRAMS 342
                                               ***********************66677888899*********************************** PP

                                 TIGR01536 333 eptairasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeealelpeaselaekklllqak 401
                                               ep+  +++i+ ylls++++++ v+Vv sG+GaDE+f+GY+++  + ++   e    +  +++ ++ ++ 
  lcl|NCBI__GCF_000020625.1:WP_012504711.1 343 EPMVSHDVIGFYLLSREVSQH-VRVVQSGQGADEVFAGYHWYPPMMNTPPTE----AYSTYSGVFFDRD 406
                                               *********************.**********************99998887....2234566788999 PP

                                 TIGR01536 402 lakeselkellkakleeelkekeelkkelkeeseleellrldlelllsdl.lrakDrvsmahslEvRvP 469
                                               +++  +  +    + +++ + ++++++   +e+ ++++lrld + +l d+ +++ D ++ma++lE+RvP
  lcl|NCBI__GCF_000020625.1:WP_012504711.1 407 FNEYRQAVNSSFITEDHAAAFVRNHFAMPGAEEPIDKALRLDSTIMLVDDpVKRVDNMTMAWGLEARVP 475
                                               99999998888888899999999999999999**********9988877626666************** PP

                                 TIGR01536 470 flDkelvelalsippelklrdgkeKvlLreaaeellPeeileRkKea 516
                                               flD+elvela++ip+e+k++dg  K++L+e+ ++++P+e+ +R+K  
  lcl|NCBI__GCF_000020625.1:WP_012504711.1 476 FLDHELVELAAKIPAEYKVKDG-GKYVLKEVGRRIIPHEVIDRPKGY 521
                                               ********************98.7********************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (592 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 12.94
//
[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