Alignments for a candidate for gatB in Flavobacterium glycines Gm-149

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Flavobacterium glycines Gm-149

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (uncharacterized)
to candidate WP_066324791.1 BLR17_RS07435 bifunctional amidotransferase subunit GatB/aspartate--tRNA ligase AspS

Query= curated2:Q6MDF6
         (494 letters)



>NCBI__GCF_900100165.1:WP_066324791.1
          Length = 1109

 Score =  253 bits (647), Expect = 2e-71
 Identities = 168/483 (34%), Positives = 252/483 (52%), Gaps = 32/483 (6%)

Query: 12  DWEAVIGLEIHVELNTKSKLFSVAPNHFGDEPNTNITEVCTGMPGSLPVLNKEAVRKAVQ 71
           D E VIGLE HV LNTK+KLF   PN   + PN NI  VCTG  G LP +NKEAV KA+ 
Sbjct: 14  DLELVIGLETHVRLNTKTKLFCSCPNQEIETPNQNICSVCTGQMGVLPAVNKEAVTKAIY 73

Query: 72  FGCAIQAEVA-KFSKFDRKSYFYPDSPRNFQITQYDQPIVKGGTVIAEVN-GKEKSFAVN 129
           FG A+ +  + +   +DRK Y YPD+P+N QITQ+  PI+  G V    N G + +  + 
Sbjct: 74  FGKAVDSSFSNEVISWDRKHYEYPDNPKNIQITQFHNPIIPDGHVSCYRNDGTQFTVNLT 133

Query: 130 RVHLEDDAGMLKHFSTFAGVDYNRAGSPLIEIVSEPCIHTPEEAVAYAMAIKAILQYIDA 189
           +VH+E+DA  L H    + VD+N+AG PLIEIV+EPCI   E+A  YA  I+ I+Q +  
Sbjct: 134 QVHIEEDAAKLMHEKKISLVDFNKAGVPLIEIVTEPCIRNIEDASTYAQYIQRIVQNLGI 193

Query: 190 SDCNMEEGSLRIDTNISVRLKGEQGLRNKIEIKNMNSFSFMELAIKSEINRQIQAYLSHP 249
           S+ N+E+G  + D ++S+R K    L  + EIKN+NSF FM  A+K E+ +Q   ++ H 
Sbjct: 194 SEANLEKGEFKSDVSVSLRKKDSNDLNPRTEIKNLNSFKFMVEALKEEVEKQFNYFVEHK 253

Query: 250 TKPHDQIIAQATYRWDPEKQETVLMRRKESADDYRYFPEPDLVPIILTDSYIEEIRQSLP 309
               D    Q T  WD E ++T  MR+KE   DYR+  EPDL P +   + IE I+    
Sbjct: 254 EFRPD----QTTVLWDAELKQTKTMRKKEFEADYRFISEPDL-PFVNIKAEIEAIKVDAS 308

Query: 310 ELPLQRERRYTKEMGLSAHQAFALTSDKALADYFEEALKTCSNSRSLSNWLLVEFPGRLK 369
            LP   E       G+    A   T+D   +  F     T +N  +  +++       +K
Sbjct: 309 ALPYAVESILING-GVLPQDAKFFTADALRSRTF----VTLNNEINDPSFVAKTLANNVK 363

Query: 370 -EGGQNVKSINLPPSHIASLINLIEKGTITGKIAKSVADEMVAQPGKDPAEIVAGNPDYQ 428
            E    + +I     H+ ++  L +   IT  + ++     +A   KD       N DY 
Sbjct: 364 AEDYAKIHNI----EHLVTIFVLFKAEKITAVLVQNA----IAGYLKDQ------NFDYN 409

Query: 429 PLNDQN-----EVERYVDQVLAENNQSIVDYRAGRDKAFAYLVGQVMKLCKGKASPSLVN 483
              ++N     +++  + +V+AEN     D  AG       LVG+V+ +    A+  ++ 
Sbjct: 410 KYFEENTISEEKIQEVISKVIAENKAVAKDIAAGDQGKAGILVGKVLGVIGKGANGKVIR 469

Query: 484 ELL 486
           +++
Sbjct: 470 QII 472


Lambda     K      H
   0.315    0.132    0.379 

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: 1224
Number of extensions: 47
Number of successful extensions: 5
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: 494
Length of database: 1109
Length adjustment: 40
Effective length of query: 454
Effective length of database: 1069
Effective search space:   485326
Effective search space used:   485326
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)

Align candidate WP_066324791.1 BLR17_RS07435 (bifunctional amidotransferase subunit GatB/aspartate--tRNA ligase AspS)
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.3135073.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.3e-107  346.2   9.3   2.4e-107  345.4   9.3    1.4  1  NCBI__GCF_900100165.1:WP_066324791.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900100165.1:WP_066324791.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  345.4   9.3  2.4e-107  2.4e-107       3     480 ..      14     476 ..      12     477 .. 0.92

  Alignments for each domain:
  == domain 1  score: 345.4 bits;  conditional E-value: 2.4e-107
                             TIGR00133   3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskivse 75 
                                           + elviGlE+Hv lntk+KlFc+c+n+  e +pN+n+c vc g+ G+lP +Nkeav+kA+  ++a++s   +e
  NCBI__GCF_900100165.1:WP_066324791.1  14 DLELVIGLETHVRLNTKTKLFCSCPNQEIE-TPNQNICSVCTGQMGVLPAVNKEAVTKAIYFGKAVDSSFSNE 85 
                                           679************************999.9***************************************** PP

                             TIGR00133  76 vsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykesdkdkqslvD 147
                                           v+ +dRKhY YpD Pk+ qitq++ Pi  dG+++   +++   +++++++h+EeD++k++++    +k+slvD
  NCBI__GCF_900100165.1:WP_066324791.1  86 VISWDRKHYEYPDNPKNIQITQFHNPIIPDGHVSCYRNDGTqFTVNLTQVHIEEDAAKLMHE----KKISLVD 154
                                           **********************************9887766269***************999....459**** PP

                             TIGR00133 148 fNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqekegtrvEiKN 220
                                           fN++gvPL+EiVt+P ++++++a  + + +++i++ l+is+++le+G +++Dv vs+r k +++   r EiKN
  NCBI__GCF_900100165.1:WP_066324791.1 155 FNKAGVPLIEIVTEPCIRNIEDASTYAQYIQRIVQNLGISEANLEKGEFKSDVSVSLRKKDSNDLNPRTEIKN 227
                                           ************************************************************************* PP

                             TIGR00133 221 lnslksiekaieyEieRqkkllkkgeev..kqetrafdekksitvslRkKeeseDYRYfpePdlppieideev 291
                                           lns+k + +a++ E+e+q + + + +e    q t  +d + ++t ++RkKe ++DYR++ ePdlp ++i+ e+
  NCBI__GCF_900100165.1:WP_066324791.1 228 LNSFKFMVEALKEEVEKQFNYFVEHKEFrpDQTTVLWDAELKQTKTMRKKEFEADYRFISEPDLPFVNIKAEI 300
                                           **********************9997762269999*************************************6 PP

                             TIGR00133 292 vkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepklavnWileellgeLnkkk 364
                                            +  ++     lP a  + +  + g+  +dak  ++d+   ++f ++++ i++p  +++ + +++++e ++k 
  NCBI__GCF_900100165.1:WP_066324791.1 301 -EA-IKVDASALPYAV-ESILINGGVLPQDAKFFTADALRSRTFVTLNNEINDPSFVAKTLANNVKAEDYAK- 369
                                           .55.888899999865.5677889*****************************9999988888887765544. PP

                             TIGR00133 365 islaeallkpeelaeliklikegkisqksakelleellen.kkdpkklieklgliqisdekelvkiveevike 436
                                                 + + e+l+++  l+k++ki++  +++ +   l++ + d +k  e++       e+++++++ +vi+e
  NCBI__GCF_900100165.1:WP_066324791.1 370 ------IHNIEHLVTIFVLFKAEKITAVLVQNAIAGYLKDqNFDYNKYFEENT----ISEEKIQEVISKVIAE 432
                                           ......23345999999***************999988773668888888765....45679*********** PP

                             TIGR00133 437 npkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                           n+    +  +g +   ++lvG+v+      a+ k + +++ ++l
  NCBI__GCF_900100165.1:WP_066324791.1 433 NKAVAKDIAAGDQGKAGILVGKVLGVIGKGANGKVIRQIIIDQL 476
                                           *99999999***************99988899999999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (1109 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: 30.45
//
[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:

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 2024 update 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 original 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