Alignments for a candidate for gatB in Frankia alni ACN14a

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Frankia alni ACN14a

Align glutamyl-tRNA^Gln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate WP_011606921.1 FRAAL_RS25500 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

Query= metacyc::MONOMER-13956
         (476 letters)



>NCBI__GCF_000058485.1:WP_011606921.1
          Length = 505

 Score =  396 bits (1017), Expect = e-114
 Identities = 212/484 (43%), Positives = 304/484 (62%), Gaps = 14/484 (2%)

Query: 3   FETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAMKA 62
           +E VIGLE HVEL T SK+F   PT FGAE NTQ   + LG PG LPV+N+ AV FA+  
Sbjct: 20  YEPVIGLETHVELGTVSKMFCGCPTAFGAEPNTQVCPVCLGLPGALPVVNEAAVRFAVMI 79

Query: 63  AMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEVGGKTKRIGITRLH 122
            +AL+C+IA+  +F RKNYFYPD PK +QISQ+D+P+  +GW+++EV G+  R+GITR+H
Sbjct: 80  GLALHCDIASWCRFARKNYFYPDMPKNFQISQYDEPLCTDGWLDVEVDGEVHRVGITRVH 139

Query: 123 LEEDAGKLTHTGDG--------YSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSI 174
           +EED GK  H G          +SLVD+NR G PLVEIV+EPD+R+PE A AY+++L+ +
Sbjct: 140 MEEDTGKSLHVGGATGRIHGATHSLVDYNRAGIPLVEIVTEPDVRSPEVARAYVDELREL 199

Query: 175 IQYTGVSDCKMEEGSLRCDANISL--RPIGQE---EFGTKTELKNLNSFAFVQKGLEHEE 229
           I+   VSD +ME+GSLRCDAN+SL  RP   E    FGT+TE KNLNS   V++ + +E 
Sbjct: 200 IRALDVSDVRMEQGSLRCDANVSLRRRPAPGEPDAPFGTRTETKNLNSLRSVERAVRYEI 259

Query: 230 KRQEQVLLSGFFIQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERV 289
            RQ   L  G  I QETR +DEA+ +T   R KE + DYRYFPEPDL  L + +++ + +
Sbjct: 260 SRQAGRLDDGERILQETRHFDEASGRTSPGRSKEEATDYRYFPEPDLTPLALPEQYVDEL 319

Query: 290 KASIPELPDERRKRYIEELGFAAYDAMVLTLTKEMADFFEETVQKGAEAKQASNWLMGEV 349
           +A +PELP  RR R + E G+   D   +     + D  E+TV  GA    A  W + E+
Sbjct: 320 RAGLPELPAARRARLVAEHGYTGRDLTDMR-NAGVLDLVEQTVAAGATPAAARKWWLNEL 378

Query: 350 SAYLNAEQKELADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGDAEKIVKEKG 409
           +        + +++A++P  +A +  L+  G ++  +A+KV   ++   G  +++V  +G
Sbjct: 379 ARRAADAGSQPSELAISPADVARITVLVAGGELTDALARKVIDGVLAGEGTPDEVVAGRG 438

Query: 410 LVQISDEGVLLKLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNKIL 469
           L  ++D+G L   V  A+   P   E  + GK  A+G LVG +MKA +GQA+   V  +L
Sbjct: 439 LAVVADDGALTAAVDAAIAAAPDIAEKVRGGKVNAVGPLVGAVMKAMRGQADAASVRGLL 498

Query: 470 LEEI 473
           LE +
Sbjct: 499 LERL 502


Lambda     K      H
   0.314    0.134    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: 600
Number of extensions: 23
Number of successful extensions: 4
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: 476
Length of database: 505
Length adjustment: 34
Effective length of query: 442
Effective length of database: 471
Effective search space:   208182
Effective search space used:   208182
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_011606921.1 FRAAL_RS25500 (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.3440585.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.7e-145  468.8   0.0   9.9e-145  468.6   0.0    1.0  1  NCBI__GCF_000058485.1:WP_011606921.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000058485.1:WP_011606921.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  468.6   0.0  9.9e-145  9.9e-145       3     480 ..      19     502 ..      17     503 .. 0.97

  Alignments for each domain:
  == domain 1  score: 468.6 bits;  conditional E-value: 9.9e-145
                             TIGR00133   3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskivse 75 
                                            ye viGlE+Hv l+t sK+Fc c++ +   +pNt+vcpvclglPGalPv+N+ av++A++++lal++ i   
  NCBI__GCF_000058485.1:WP_011606921.1  19 RYEPVIGLETHVELGTVSKMFCGCPTAFGA-EPNTQVCPVCLGLPGALPVVNEAAVRFAVMIGLALHCDIA-S 89 
                                           6899************************99.**************************************65.6 PP

                             TIGR00133  76 vsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesdk.....dkq 143
                                              F+RK+YfYpD+Pk++qi+q+d P+++dG l++e++++ +++gi+r+h+EeDtgks + +  +     +++
  NCBI__GCF_000058485.1:WP_011606921.1  90 WCRFARKNYFYPDMPKNFQISQYDEPLCTDGWLDVEVDGEVHRVGITRVHMEEDTGKSLHVGGATgrihgATH 162
                                           ************************************************************987766677899* PP

                             TIGR00133 144 slvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlk.....Gqek 211
                                           slvD+NR+g+PL+EiVt+Pd++s++ ara++ +lr+++r l++sd  +e+Gs+R+D+Nvs+r +      +  
  NCBI__GCF_000058485.1:WP_011606921.1 163 SLVDYNRAGIPLVEIVTEPDVRSPEVARAYVDELRELIRALDVSDVRMEQGSLRCDANVSLRRRpapgePDAP 235
                                           **************************************************************87777333567 PP

                             TIGR00133 212 egtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlpp 284
                                           +gtr E KNlnsl+s+e+a+ yEi Rq   l +ge + qetr+fde++ +t   R+Kee++DYRYfpePdl+p
  NCBI__GCF_000058485.1:WP_011606921.1 236 FGTRTETKNLNSLRSVERAVRYEISRQAGRLDDGERILQETRHFDEASGRTSPGRSKEEATDYRYFPEPDLTP 308
                                           9************************************************************************ PP

                             TIGR00133 285 ieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepklavnWileell 357
                                           + + e++v+e +++ lpelP a+r+rl+ e g   +d    + ++ +ld  e+ v + ++p +a +W l+el+
  NCBI__GCF_000058485.1:WP_011606921.1 309 LALPEQYVDE-LRAGLPELPAARRARLVAEHGYTGRDLTD-MRNAGVLDLVEQTVAAGATPAAARKWWLNELA 379
                                           **********.*********************99999754.57899*************************** PP

                             TIGR00133 358 geLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkklieklgliqisdekelvkiv 430
                                           ++  +   + +e +++p ++a++  l+  g++++  a+++++ +l  ++ p++++  +gl  + d+ +l+++v
  NCBI__GCF_000058485.1:WP_011606921.1 380 RRAADAGSQPSELAISPADVARITVLVAGGELTDALARKVIDGVLAGEGTPDEVVAGRGLAVVADDGALTAAV 452
                                           ************************************************************************* PP

                             TIGR00133 431 eevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                           +++i+  p+  ek + gk +a++ lvG vmk  +g+ad+++v  ll e+l
  NCBI__GCF_000058485.1:WP_011606921.1 453 DAAIAAAPDIAEKVRGGKVNAVGPLVGAVMKAMRGQADAASVRGLLLERL 502
                                           ********************************************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (505 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 36.46
//
[ok]

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

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Steps (tab-delimited)
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Protein sequences (fasta format)
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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