Alignments for a candidate for gatD in Haloferax volcanii DS2

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatD in Haloferax volcanii DS2

Align glutamyl-tRNA(Gln) amidotransferase subunit D (EC 6.3.5.7) (characterized)
to candidate WP_004042487.1 C498_RS07595 Glu-tRNA(Gln) amidotransferase subunit GatD

Query= metacyc::MONOMER-14998
         (435 letters)



>NCBI__GCF_000337315.1:WP_004042487.1
          Length = 415

 Score =  357 bits (917), Expect = e-103
 Identities = 202/419 (48%), Positives = 264/419 (63%), Gaps = 14/419 (3%)

Query: 16  IDVGDMVLVEKPDVTYEGMVLDRADDADDRHIVLKLENGYNIGVEISDARIELLEKG--- 72
           ++ GD V V + DVT EG+++     + + H+V+KL+ GYN+G+    A +++LE     
Sbjct: 1   MNAGDRVRVTRADVTNEGVLMP---SSTEDHLVVKLDGGYNVGIAREGADVDVLETDVYD 57

Query: 73  -SEPRIELPPVEAAE-DPELPDVSIISTGGTVASIIDYRTGAVHPAFTADDLLRANPELL 130
             + + E       E D +LP +S+ISTGGT+AS +DYRTGAV   F A D+LRA P+L 
Sbjct: 58  IEDAQSEGDGTSEIEFDDDLPTISLISTGGTIASTVDYRTGAVTAQFDAKDVLRAVPDLA 117

Query: 131 DIANIRGRAVFNILSENMKPEYWVETARAVYGEIKDGADGVVVAHGTDTMHYTSAALSFM 190
             AN RGR V NILSENM  + WV+ A AV  EI+ GADGVVV HGTDTM ++++A+SFM
Sbjct: 118 GRANYRGRVVANILSENMTTDVWVDLAEAVAEEIEGGADGVVVMHGTDTMQFSASAMSFM 177

Query: 191 LRTPVPVVFTGAQRSSDRPSSDASLNIQCSVRAATSEIAEVTVCMHATMDDLSCHLHRGV 250
           L TPVP+VFTG+QRS+DRPSSD  +N  C+V AA +E AEV VCMHA+  D  C LH G 
Sbjct: 178 LDTPVPIVFTGSQRSADRPSSDNVMNAVCAVEAAKAEAAEVMVCMHASESDDVCALHEGT 237

Query: 251 KVRKMHTSRRDTFRSMNALPLAEVTPDGIKI-LEENYRKRGSDELELSDRVEERVAFIKS 309
           +VRK HTSRRD F ++ A PL EV  +  ++    +Y  R   +L L   +E  V  +K 
Sbjct: 238 RVRKNHTSRRDAFETVGAKPLGEVDYEAEEVTFRRDYTPRCEADLALHADIESEVELVKF 297

Query: 310 YPGISPDIIKWHLDEGYRGIVIEGTGLGHCPDTLIPVIGEAHDMGVPVAMTSQCLNGRVN 369
            PG+ P  +  +LDE   G+VIEGTGLGH    LIP   E  + G  VAMTSQCL GRV 
Sbjct: 298 TPGMDPAALD-YLDE-KAGVVIEGTGLGHVHTDLIPQFEELVEGGTVVAMTSQCLEGRVC 355

Query: 370 MNVYSTGRRLLQAGVIPCDDMLPEVAYVKMCWVLGQTDDPEMAREMMRENIAGEINERT 428
             VY TGR LL AGV+   D LP  A VK+ W L    DP    + M  N+ GE+ +R+
Sbjct: 356 DRVYDTGRDLLDAGVVEAGDTLPGTAKVKLMWALANVADP---TDAMGRNLEGELTQRS 411


Lambda     K      H
   0.318    0.135    0.395 

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: 534
Number of extensions: 21
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: 435
Length of database: 415
Length adjustment: 32
Effective length of query: 403
Effective length of database: 383
Effective search space:   154349
Effective search space used:   154349
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_004042487.1 C498_RS07595 (Glu-tRNA(Gln) amidotransferase subunit GatD)
to HMM TIGR02153 (gatD: glutamyl-tRNA(Gln) amidotransferase, subunit D (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/TIGR02153.hmm
# target sequence database:        /tmp/gapView.1286967.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02153  [M=405]
Accession:   TIGR02153
Description: gatD_arch: glutamyl-tRNA(Gln) amidotransferase, subunit D
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.8e-153  495.3   0.4   6.7e-153  495.1   0.4    1.0  1  NCBI__GCF_000337315.1:WP_004042487.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000337315.1:WP_004042487.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  495.1   0.4  6.7e-153  6.7e-153       3     404 ..      17     412 ..      15     413 .. 0.94

  Alignments for each domain:
  == domain 1  score: 495.1 bits;  conditional E-value: 6.7e-153
                             TIGR02153   3 eGvvlpstelseediivlklknGYnvgvkkeeveeievleeekeek.....lekleeeiekkeelekvsilst 70 
                                           eGv++ps   s+ed++v+kl+ GYnvg+++e ++ ++vle+   +      +   ++eie +++l+++s++st
  NCBI__GCF_000337315.1:WP_004042487.1  17 EGVLMPS---STEDHLVVKLDGGYNVGIAREGAD-VDVLETDVYDIedaqsEGDGTSEIEFDDDLPTISLIST 85 
                                           8******...7789***************98765.55555443322111226677889999************ PP

                             TIGR02153  71 GGtiaskvdYetGavkpaltaeelleavpelkeianikaravlnilsenmkPesWikiaeevakaleegadgv 143
                                           GGtias vdY+tGav+++++a+++l+avp+l   an ++r v nilsenm+ + W+ +ae+va+++e gadgv
  NCBI__GCF_000337315.1:WP_004042487.1  86 GGTIASTVDYRTGAVTAQFDAKDVLRAVPDLAGRANYRGRVVANILSENMTTDVWVDLAEAVAEEIEGGADGV 158
                                           ************************************************************************* PP

                             TIGR02153 144 vvahGtDtmaytaaaLsFmlkklpvPvvlvGaqRssDRPssDaalnliaavkvakediaevvvvmhgetsDty 216
                                           vv hGtDtm+++a+a+sFml + pvP+v++G+qRs+DRPssD+++n ++av++ak + aev+v+mh++ sD++
  NCBI__GCF_000337315.1:WP_004042487.1 159 VVMHGTDTMQFSASAMSFMLDT-PVPIVFTGSQRSADRPSSDNVMNAVCAVEAAKAEAAEVMVCMHASESDDV 230
                                           **********************.************************************************** PP

                             TIGR02153 217 vlvhrgvkvrkmhtsRRDaFksinslPlakvdpkekeiellredyrkrgekelelkdkleekvalvkfyPGls 289
                                           +++h g++vrk+htsRRDaF+ + ++Pl++vd++  e++++r+dy+ r e +l+l++++e+ v lvkf+PG++
  NCBI__GCF_000337315.1:WP_004042487.1 231 CALHEGTRVRKNHTSRRDAFETVGAKPLGEVDYEA-EEVTFRRDYTPRCEADLALHADIESEVELVKFTPGMD 302
                                           *********************************65.78899******************************** PP

                             TIGR02153 290 peilealvdkgykgivieGtGlGhvsedlievikkavddgvvvvmtsqclyGrvnlnvYstGRellkaGviea 362
                                           p  l++l +k   g+vieGtGlGhv +dli++++++v+ g+vv+mtsqcl Grv+++vY+tGR+ll+aGv+ea
  NCBI__GCF_000337315.1:WP_004042487.1 303 PAALDYLDEKA--GVVIEGTGLGHVHTDLIPQFEELVEGGTVVAMTSQCLEGRVCDRVYDTGRDLLDAGVVEA 373
                                           *****876666..************************************************************ PP

                             TIGR02153 363 edmlpevayvklmwvLgqteeleevrkllkknlageieertl 404
                                           +d+lp +a vklmw L+++ +     + + +nl ge+++r++
  NCBI__GCF_000337315.1:WP_004042487.1 374 GDTLPGTAKVKLMWALANVAD---PTDAMGRNLEGELTQRSV 412
                                           *******************99...55679********99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (415 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: 15.05
//
[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