GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatB in Epibacterium ulvae U95

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate WP_090218450.1 CV091_RS00950 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

Query= SwissProt::Q9RF06
         (475 letters)



>NCBI__GCF_002796795.1:WP_090218450.1
          Length = 503

 Score =  392 bits (1007), Expect = e-113
 Identities = 206/483 (42%), Positives = 307/483 (63%), Gaps = 15/483 (3%)

Query: 3   FETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAMRA 62
           +E VIG+EVH ++ +++K+FS +   FGAEPNSN   +D A PG+LPV+N+  V+  +R 
Sbjct: 21  WELVIGMEVHAQVSSNAKLFSGASTKFGAEPNSNVAFVDAAMPGMLPVINEFCVEQTVRT 80

Query: 63  AMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEV-DGETKRIGITRL 121
            + L  EI   S FDRKNYFYPD P+ YQISQ   PI   G + +E+ DG  + + + R+
Sbjct: 81  GLGLKAEINLWSAFDRKNYFYPDLPQGYQISQLYHPIVGEGEVLVELGDGTARNVRVERI 140

Query: 122 HMEEDAGKSTHKGE--YSLVDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYTGV 179
           HME+DAGKS H  +   S VDLNR G  L+EIVS+PDIR P+EA AY+ KLR I+QY G 
Sbjct: 141 HMEQDAGKSIHDMDPNMSFVDLNRTGVCLMEIVSQPDIRGPEEAAAYIAKLRQIMQYLGT 200

Query: 180 SDVKMEEGSLRCDANISLRPYGQ-EKF---------GTKAELKNLNSFNYVRKGLEYEEK 229
            D  M+ G+LR D N+S+   GQ EKF         GT+ E+KN+NS  ++++ +E E +
Sbjct: 201 CDGNMQNGNLRADVNVSVCLPGQYEKFQETGDFSHLGTRCEIKNMNSMRFIQQAIEVEAR 260

Query: 230 RQEEELLSGGEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVR 289
           RQ   + +GG+I QETR +D   G+T  MR KE + DYRYFP+PD++PL I+  W + + 
Sbjct: 261 RQIAIIEAGGKIDQETRLYDPDKGETRSMRSKEEAHDYRYFPDPDLLPLEIEQDWVDDIA 320

Query: 290 QTIPELPDERKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVN 349
             +PELPD++K+++++E  L  YDA VLT     + +FE  +  G   KL +NW++  + 
Sbjct: 321 AKLPELPDQKKSRFISEFSLTDYDASVLTAEVAAASYFEE-VAQGRTGKLAANWVINELF 379

Query: 350 EYLNKNQVELLDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGL 409
             L K+  ++ ++ ++P  L G+I LI    +S KIAK +F  +  +GG+  +I+E+ G+
Sbjct: 380 GRLKKDDKDITESPVSPAQLGGIIDLISSDAISGKIAKDLFEIVYTEGGDPAEIVEERGM 439

Query: 410 VQISDEATLLKFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLK 469
            Q++D   +   ++E +  N   VE  K    K  G+ VGQ+MKA+ G+ANP+ VNQL+ 
Sbjct: 440 KQVTDTGAIEAALDEIIAANPAQVEKAKENP-KLAGWFVGQVMKATGGKANPKAVNQLVA 498

Query: 470 QEL 472
            +L
Sbjct: 499 AKL 501


Lambda     K      H
   0.313    0.133    0.373 

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: 634
Number of extensions: 23
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: 475
Length of database: 503
Length adjustment: 34
Effective length of query: 441
Effective length of database: 469
Effective search space:   206829
Effective search space used:   206829
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 52 (24.6 bits)

Align candidate WP_090218450.1 CV091_RS00950 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB)
to HMM TIGR00133 (gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit (EC 6.3.5.-))

# 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/TIGR00133.hmm
# target sequence database:        /tmp/gapView.3077794.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00133  [M=481]
Accession:   TIGR00133
Description: gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.6e-158  511.7   0.0     1e-157  511.5   0.0    1.0  1  NCBI__GCF_002796795.1:WP_090218450.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002796795.1:WP_090218450.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  511.5   0.0    1e-157    1e-157       3     480 ..      20     501 ..      18     502 .. 0.95

  Alignments for each domain:
  == domain 1  score: 511.5 bits;  conditional E-value: 1e-157
                             TIGR00133   3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskivse 75 
                                           ++elviG+EvH q+  ++KlF+ +s+++   +pN+nv  v+ ++PG lPv+N+  v++ +  +l l+++i+  
  NCBI__GCF_002796795.1:WP_090218450.1  20 DWELVIGMEVHAQVSSNAKLFSGASTKFGA-EPNSNVAFVDAAMPGMLPVINEFCVEQTVRTGLGLKAEIN-L 90 
                                           789*************************99.**************************************76.5 PP

                             TIGR00133  76 vsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykesdkdkqslvD 147
                                            s FdRK+YfYpDlP+gyqi+q + Pi+ +G++ +el ++  +++++er+h+E+D+gks +  +  +++s+vD
  NCBI__GCF_002796795.1:WP_090218450.1  91 WSAFDRKNYFYPDLPQGYQISQLYHPIVGEGEVLVELGDGTaRNVRVERIHMEQDAGKSIHDMD--PNMSFVD 161
                                           ************************************9765449******************966..79***** PP

                             TIGR00133 148 fNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGq..........e 210
                                           +NR+gv L+EiV++Pd++ ++ea+a++ klrqi++yl+  dg++++G++R+DvNvs+ l Gq          +
  NCBI__GCF_002796795.1:WP_090218450.1 162 LNRTGVCLMEIVSQPDIRGPEEAAAYIAKLRQIMQYLGTCDGNMQNGNLRADVNVSVCLPGQyekfqetgdfS 234
                                           *********************************************************9988733332222234 PP

                             TIGR00133 211 kegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlp 283
                                           + gtr EiKN+ns++ i++aie E  Rq+++++ g ++ qetr +d  k  t s+R+Kee++DYRYfp+Pdl 
  NCBI__GCF_002796795.1:WP_090218450.1 235 HLGTRCEIKNMNSMRFIQQAIEVEARRQIAIIEAGGKIDQETRLYDPDKGETRSMRSKEEAHDYRYFPDPDLL 307
                                           5799********************************************************************* PP

                             TIGR00133 284 pieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepklavnWileel 356
                                           p+ei++++v++ +++klpelP++k+ r+ +e+ l ++da vl++++  +++feev++  +  kla+nW+++el
  NCBI__GCF_002796795.1:WP_090218450.1 308 PLEIEQDWVDD-IAAKLPELPDQKKSRFISEFSLTDYDASVLTAEVAAASYFEEVAQGRTG-KLAANWVINEL 378
                                           ***********.*******************************************997776.*********** PP

                             TIGR00133 357 lgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkklieklgliqisdekelvki 429
                                            g+L+k + +++e+ ++p +l  +i+li+ + is+k+ak+l+e + ++++dp +++e++g+ q++d+ ++ ++
  NCBI__GCF_002796795.1:WP_090218450.1 379 FGRLKKDDKDITESPVSPAQLGGIIDLISSDAISGKIAKDLFEIVYTEGGDPAEIVEERGMKQVTDTGAIEAA 451
                                           ************************************************************************* PP

                             TIGR00133 430 veevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                           ++e+i+ np +vek k++  k+ +++vGqvmk t g+a+pk v++l+  +l
  NCBI__GCF_002796795.1:WP_090218450.1 452 LDEIIAANPAQVEKAKEN-PKLAGWFVGQVMKATGGKANPKAVNQLVAAKL 501
                                           *************98875.56889**********************98877 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (503 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: 00:00:00.01
# Mc/sec: 23.34
//
[ok]

This GapMind analysis is from Jul 26 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:

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:

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:

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:

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