Alignments for a candidate for gatB in Methylocella silvestris BL2

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Methylocella silvestris BL2

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate WP_012589778.1 MSIL_RS03800 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B

Query= SwissProt::Q9RF06
         (475 letters)



>NCBI__GCF_000021745.1:WP_012589778.1
          Length = 495

 Score =  408 bits (1049), Expect = e-118
 Identities = 216/478 (45%), Positives = 303/478 (63%), Gaps = 10/478 (2%)

Query: 3   FETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAMRA 62
           FE VIG+E+H ++ + SK+FS +   FG EPN++ +++D A PG+LPV+N+  V  A+R 
Sbjct: 18  FEIVIGMEIHAQVTSRSKLFSGASTEFGGEPNAHVSLVDAAMPGMLPVINQECVAQAVRT 77

Query: 63  AMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEVDG-ETKRIGITRL 121
            + L  +I   S FDRKNYFYPD P+ YQISQ+  PI   G + ++V   E  ++GI RL
Sbjct: 78  GLGLEAQINLRSVFDRKNYFYPDLPQGYQISQYKSPIVGEGVVAVDVSPTEQIKVGIERL 137

Query: 122 HMEEDAGKSTH--KGEYSLVDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYTGV 179
           H+E+DAGKS H      SLVDLNR G  L+EIVS+PD+RS  EA AY+ KLR+I++Y G 
Sbjct: 138 HLEQDAGKSLHDQSATESLVDLNRSGVALMEIVSKPDMRSSDEARAYVTKLRTILRYIGS 197

Query: 180 SDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELLSGG 239
            D  ME+GSLR D N+S+R  G E  GT+ E+KN+NS  ++ + +E E +RQ   +  GG
Sbjct: 198 CDGNMEQGSLRADVNVSVRRPG-EPLGTRCEIKNVNSIRFIGQAIEVEARRQIGVIEDGG 256

Query: 240 EIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELPDER 299
            + QETR FD   G+T  MR KE + DYRYFP+PD++PL  D A+ + ++  +PELPD +
Sbjct: 257 VVQQETRLFDPGRGETRSMRSKEEAHDYRYFPDPDLLPLEFDQAYVDGLKAGLPELPDAK 316

Query: 300 KAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGA---DVKLTSNWLMGGVNEYLNKNQ 356
           K +++ E GLPAYDA VL   KE +D++E+ + HG    D KL +NWL G V  Y N   
Sbjct: 317 KERFIAEYGLPAYDAGVLVADKETADYYEAAVRHGGAKRDPKLVANWLTGDVAAYANSVG 376

Query: 357 VELLDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAA--KGGNAKQIMEDNGLVQISD 414
           + +  T + P  +A ++ LI DGT+S KIAK V   L A  K  + K I+E  GL Q++D
Sbjct: 377 LSVAQTHIKPGQIASLVDLIADGTISGKIAKDVLSILIAEEKDADPKDIVEARGLRQVTD 436

Query: 415 EATLLKFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLKQEL 472
              +   V+  +  N   V      K   +G+ VGQ+MK + G+ANPQ VN  LK +L
Sbjct: 437 TGAIAAAVDAIIKANPDKVAQ-AQAKPSMLGWFVGQVMKQTGGKANPQAVNDELKAKL 493


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: 625
Number of extensions: 32
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: 495
Length adjustment: 34
Effective length of query: 441
Effective length of database: 461
Effective search space:   203301
Effective search space used:   203301
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_012589778.1 MSIL_RS03800 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B)
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.15123.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.2e-163  530.1   0.0   2.5e-163  530.0   0.0    1.0  1  lcl|NCBI__GCF_000021745.1:WP_012589778.1  MSIL_RS03800 Asp-tRNA(Asn)/Glu-t


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021745.1:WP_012589778.1  MSIL_RS03800 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  530.0   0.0  2.5e-163  2.5e-163       3     480 ..      17     493 ..      15     494 .. 0.96

  Alignments for each domain:
  == domain 1  score: 530.0 bits;  conditional E-value: 2.5e-163
                                 TIGR00133   3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnsk 71 
                                               ++e+viG+E+H q+  +sKlF+ +s+e+   +pN +v+ v+ ++PG lPv+N+e v++A+  +l l+++
  lcl|NCBI__GCF_000021745.1:WP_012589778.1  17 DFEIVIGMEIHAQVTSRSKLFSGASTEFGG-EPNAHVSLVDAAMPGMLPVINQECVAQAVRTGLGLEAQ 84 
                                               79****************************.************************************** PP

                                 TIGR00133  72 ivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykesd 139
                                               i+   svFdRK+YfYpDlP+gyqi+q++ Pi+ +G++ ++++ +e  ++gierlhlE+D+gks + +s 
  lcl|NCBI__GCF_000021745.1:WP_012589778.1  85 IN-LRSVFDRKNYFYPDLPQGYQISQYKSPIVGEGVVAVDVSPTEqIKVGIERLHLEQDAGKSLHDQSA 152
                                               77.59***********************************98877368******************775 PP

                                 TIGR00133 140 kdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkG 208
                                                 + slvD+NRsgv L+EiV+kPd++s++eara++ klr+ilry++  dg++e+Gs+R+DvNvs+r   
  lcl|NCBI__GCF_000021745.1:WP_012589778.1 153 --TESLVDLNRSGVALMEIVSKPDMRSSDEARAYVTKLRTILRYIGSCDGNMEQGSLRADVNVSVRRP- 218
                                               ..7***************************************************************55. PP

                                 TIGR00133 209 qekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYf 277
                                                e  gtr EiKN+ns++ i +aie E  Rq+ ++++g  v+qetr fd  +  t s+R+Kee++DYRYf
  lcl|NCBI__GCF_000021745.1:WP_012589778.1 219 GEPLGTRCEIKNVNSIRFIGQAIEVEARRQIGVIEDGGVVQQETRLFDPGRGETRSMRSKEEAHDYRYF 287
                                               5789***************************************************************** PP

                                 TIGR00133 278 pePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikep. 345
                                               p+Pdl p+e+d+ +v++ +++ lpelP+ak++r+  eygl ++da vlv+d+e +d++e +v+  + + 
  lcl|NCBI__GCF_000021745.1:WP_012589778.1 288 PDPDLLPLEFDQAYVDG-LKAGLPELPDAKKERFIAEYGLPAYDAGVLVADKETADYYEAAVRHGGAKr 355
                                               *****************.99****************************************999876555 PP

                                 TIGR00133 346 ..klavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellen..kkdpkk 410
                                                 kl++nW++ +++++ n+  +s+a++ +kp ++a+l++li +g+is+k+ak++l+ l+ +    dpk 
  lcl|NCBI__GCF_000021745.1:WP_012589778.1 356 dpKLVANWLTGDVAAYANSVGLSVAQTHIKPGQIASLVDLIADGTISGKIAKDVLSILIAEekDADPKD 424
                                               56*******************************************************99884466899* PP

                                 TIGR00133 411 lieklgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkel 479
                                               ++e++gl q++d+ ++ ++v+++ik np++v + +  k ++l+++vGqvmk+t g+a+p+ v+  lk +
  lcl|NCBI__GCF_000021745.1:WP_012589778.1 425 IVEARGLRQVTDTGAIAAAVDAIIKANPDKVAQAQ-AKPSMLGWFVGQVMKQTGGKANPQAVNDELKAK 492
                                               *******************************9865.6789***********************999987 PP

                                 TIGR00133 480 l 480
                                               l
  lcl|NCBI__GCF_000021745.1:WP_012589778.1 493 L 493
                                               7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (495 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: 8.33
//
[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