Alignments for a candidate for asnB in Methylobacterium nodulans ORS 2060

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Methylobacterium nodulans ORS 2060

Align asparagine synthase (glutamine-hydrolysing) 3; EC 6.3.5.4 (characterized)
to candidate WP_015926901.1 MNOD_RS00665 N-acetylglutaminylglutamine amidotransferase

Query= CharProtDB::CH_007942
         (614 letters)



>NCBI__GCF_000022085.1:WP_015926901.1
          Length = 590

 Score =  241 bits (614), Expect = 8e-68
 Identities = 186/615 (30%), Positives = 289/615 (46%), Gaps = 41/615 (6%)

Query: 1   MCGITGWVDFKKQLVQEKQTMDRMTDTLSKRGPDDSNVWGEHHVLFGHKRLAVVDIE-GG 59
           MCGI G +        +   +  M   L  RGPD    + +  + FGH+RL+++D+    
Sbjct: 1   MCGICGEIRLDGA-PPDAAAVAAMAVPLRARGPDAGGSFAQGGIAFGHRRLSILDLSPAS 59

Query: 60  RQPMACTYKGDTYTIIYNGELYNTEDLRKELRARGHQFERTSDTEVLLHSYIEWQEDCVD 119
           +QPM     G    I++NG +YN   LR+ELRA+G+ F    DTEV+L +Y  W   CV+
Sbjct: 60  QQPMVDPGLG--LAIVFNGCIYNFRSLREELRAKGYAFFSEGDTEVILKAYHAWGPRCVE 117

Query: 120 HLNGIFAFAVWDEKRNLLFAARDRLGVKPFFYTKEGSSFLFGSEIKAILAHPDIKARVDR 179
              G+FAF +W+     +  ARDRLG+KP +Y + GS   F S + A+LA  D+   +D 
Sbjct: 118 RFYGMFAFVLWERDSGRVVIARDRLGIKPLYYAESGSRLRFASSLPALLAAGDLDRSIDP 177

Query: 180 TGLSEIFGLGPSRTPGTGIFKGIKEIRPAHALTFSKDGLNIWR-YWN-VESEKHTD---S 234
             L               I KG++++ PA  +T   DG      YW  V +E+  D   +
Sbjct: 178 AALHHYMSFHAVVPAPLTILKGVRKVPPATIITIEPDGRRRQETYWEAVVTERPDDRHMT 237

Query: 235 FDDTVANVRSLFQDAVTRQLVSDVPVCTFLSGGLDSSAITAIAAGHFEKEGKAPLHTYSI 294
             D    V +  + AV R+LVSDVPV   LSGGLDSS + A+ A    + G+  L T+SI
Sbjct: 238 ESDWCEAVLATLRKAVERRLVSDVPVGVLLSGGLDSSIVVALLA----EAGQRGLKTFSI 293

Query: 295 DYEENDKYFQASAFQPNDDGPWIEKMTEAFGTTHHKCVISQKDLVDHLEEAVLVKDLPGM 354
                   F++   +  D+  + + + E F T HH+  I     +  L  AV     P +
Sbjct: 294 G-------FESVGGEAGDEFTYSDIIAERFATDHHRIRIDSARALPALHGAVAAMSEPMV 346

Query: 355 ADVDSSLLWFCREIKKDFVVSLSGECADEIFGGYPWF----HTADVESGFP---WMRSTE 407
           +           E+ K   V  SG+ ADEIFGGY W+     + D  + +    + R   
Sbjct: 347 SHDAVGFYLLSEEVSKHVKVVQSGQGADEIFGGYHWYPPMMQSTDAVADYARVFFDRDHA 406

Query: 408 ERIKLLSDSWQKKLNLKEYVNAKYEETLAETPLLDGETGVDKARRQLFYLNMLWFMTNLL 467
           E  + LS S       + +V A +    A  P       +DKA R       +  + + +
Sbjct: 407 EMREALSPSLVDGDVSRAFVEAHFARAGAPRP-------IDKALR---IDTEIMLVDDPV 456

Query: 468 DRKDRMSMGASLEVRVPFADHRLVEYVWNIPWEMKMHDNREKGILRKALEGILPDDILYR 527
            R D M+M   LE RVPF DH LVE    +P ++K+ D   K IL++A   ++P +++ R
Sbjct: 457 KRVDNMTMAWGLEARVPFLDHDLVELAGRVPADLKIRDG-GKFILKQAGRRVVPSEVIDR 515

Query: 528 KKSPYPKTHHPEYTKG-VSEWLKTIRSQKDSVLHTLLDRKQLDQLLETEGSSFKVPWFGQ 586
            K  +P     +Y +G   + ++ + ++  +    L +R  +D+LL  E  +   P  G 
Sbjct: 516 PKGYFP-VPALKYLRGPFLDLVRDVLNEPVARERGLFNRAYVDRLL-AEPEAHMTPLRGS 573

Query: 587 LMKGPQLIAHLAQIH 601
            +    L+    Q H
Sbjct: 574 KLWQVALLEFWLQTH 588


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: 841
Number of extensions: 33
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: 590
Length adjustment: 37
Effective length of query: 577
Effective length of database: 553
Effective search space:   319081
Effective search space used:   319081
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_015926901.1 MNOD_RS00665 (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.1905085.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.7e-135  438.2   0.0   3.1e-135  438.0   0.0    1.0  1  NCBI__GCF_000022085.1:WP_015926901.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000022085.1:WP_015926901.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  438.0   0.0  3.1e-135  3.1e-135       1     516 [.       2     519 ..       2     520 .. 0.91

  Alignments for each domain:
  == domain 1  score: 438.0 bits;  conditional E-value: 3.1e-135
                             TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsnek.ev 71 
                                           Cgi g + l+ +  +  +a+++m+  l+ RGPDa g + +    + ++ghrRL+i dls + +QP+ + +   
  NCBI__GCF_000022085.1:WP_015926901.1   2 CGICGEIRLDGAPPD-AAAVAAMAVPLRARGPDAGGSFAQ---GGIAFGHRRLSILDLSPAsQQPMVDPGlGL 70 
                                           *********887555.69******************9998...8****************99*********99 PP

                             TIGR01536  72 vivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlG 144
                                           +ivfnG IYN+++Lreel++kGy F ++ DtEViL+ay++wg ++ver+ GmFAf+lw++ +g++++aRDrlG
  NCBI__GCF_000022085.1:WP_015926901.1  71 AIVFNGCIYNFRSLREELRAKGYAFFSEGDTEVILKAYHAWGPRCVERFYGMFAFVLWERDSGRVVIARDRLG 143
                                           ************************************************************************* PP

                             TIGR01536 145 ikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlq.lvptektlfkevkelepakal....dge 212
                                           ikPLYya+ +++l faS + alla+ + ++++d +al+++++++ +vp + t+ k+v++++pa       dg 
  NCBI__GCF_000022085.1:WP_015926901.1 144 IKPLYYAESGSRLRFASSLPALLAAGDLDRSIDPAALHHYMSFHaVVPAPLTILKGVRKVPPATIItiepDGR 216
                                           ********************************************999****************9999977777 PP

                             TIGR01536 213 ekleeywevekee....vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeaksevk 281
                                           ++ e+ywe+ ++e    ++++e++ +e +  +l++av++rlv+dvpvgvllSGGlDSs+v+a++++  ++ +k
  NCBI__GCF_000022085.1:WP_015926901.1 217 RRQETYWEAVVTErpddRHMTESDWCEAVLATLRKAVERRLVSDVPVGVLLSGGLDSSIVVALLAEAGQRGLK 289
                                           77788***999988888889999************************************************** PP

                             TIGR01536 282 tFsigfe..dskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasiplyllsklare 352
                                           tFsigfe  + ++ de ++   +a+ + t+h+++ i+++ +l +l+  + a+ ep+  +++++ ylls+++++
  NCBI__GCF_000022085.1:WP_015926901.1 290 TFSIGFEsvGGEAGDEFTYSDIIAERFATDHHRIRIDSARALPALHGAVAAMSEPMVSHDAVGFYLLSEEVSK 362
                                           *******87788899999******************************************************* PP

                             TIGR01536 353 kgvkVvLsGeGaDElfgGYeyfreakaeealelpeaselaekklllqaklakeselkellkakleeelkekee 425
                                           + vkVv sG+GaDE+fgGY+++  + ++ ++  +      +++++ ++  a+  e       + + +++ +e+
  NCBI__GCF_000022085.1:WP_015926901.1 363 H-VKVVQSGQGADEIFGGYHWYPPMMQSTDAV-AD-----YARVFFDRDHAEMREALSPSLVDGDVSRAFVEA 428
                                           *.*********************987777774.33.....333444444444444444444444444555666 PP

                             TIGR01536 426 lkkelkeeseleellrldlelllsdl.lrakDrvsmahslEvRvPflDkelvelalsippelklrdgkeKvlL 497
                                           ++++  + + ++++lr d+e +l d+ +++ D ++ma++lE+RvPflD++lvela ++p++lk+rdg  K++L
  NCBI__GCF_000022085.1:WP_015926901.1 429 HFARAGAPRPIDKALRIDTEIMLVDDpVKRVDNMTMAWGLEARVPFLDHDLVELAGRVPADLKIRDG-GKFIL 500
                                           666677779***********99887626666**********************************98.7**** PP

                             TIGR01536 498 reaaeellPeeileRkKea 516
                                           ++a ++++P+e+ +R+K  
  NCBI__GCF_000022085.1:WP_015926901.1 501 KQAGRRVVPSEVIDRPKGY 519
                                           ****************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (590 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 22.09
//
[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