Alignments for a candidate for argA in Teredinibacter turnerae T7901

GapMind for Amino acid biosynthesis

Alignments for a candidate for argA in Teredinibacter turnerae T7901

Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate WP_015817743.1 TERTU_RS01670 amino-acid N-acetyltransferase

Query= BRENDA::P22567
         (432 letters)



>NCBI__GCF_000023025.1:WP_015817743.1
          Length = 441

 Score =  420 bits (1080), Expect = e-122
 Identities = 217/433 (50%), Positives = 295/433 (68%), Gaps = 3/433 (0%)

Query: 3   DYVNWLRHASPYINSHRDRTFVVMLPGEGVEHPNFGNIVHDLVLLHSLGARLVLVHGSRP 62
           +Y+ W RH SPYINSHR +TFVV+LPG+ +   NF NI++DL LL SLG RLV+VHG+R 
Sbjct: 7   NYIQWFRHTSPYINSHRGKTFVVLLPGDCISQDNFPNIINDLTLLSSLGVRLVVVHGARR 66

Query: 63  QIEARLAARGLAPRYHRDLRVTDAPTLECVIDAVGSLRIAIEARLSMDMAASPMQGARLR 122
           QI+ +LA       +H+ +R+T    +  V+ A+G  R  IEA  S  +  SPM G+++R
Sbjct: 67  QIDEQLAVINSETEFHKGVRITTREQMGEVLKAIGHARFTIEAAFSSGLPDSPMYGSKIR 126

Query: 123 VAGGNLVTARPIGVVEGVDYHHTGEVRRIDRKGIGRLLDERSIVLLSPLGYSPTGEIFNL 182
           V  GN VTA P GV++G+D+  TG+VR +D  GI  +LD+ S+ L+SPLGYS TGE FNL
Sbjct: 127 VRCGNFVTAMPQGVIDGIDHQLTGKVRSVDASGIRAMLDQNSLALVSPLGYSLTGEAFNL 186

Query: 183 ACEDVAMRAAIDLEAEKLILYGAEQGLLDASGKLVRELRPQQVPAHL---QRLGNSYQAE 239
           +  DVA+  A  L A+KLI Y  +  + D+ G+  REL   Q    L   Q+   S    
Sbjct: 187 SFADVAIAIANALRADKLIAYNDDGPITDSQGEQFRELTLLQCERFLLEKQQHNRSNTYF 246

Query: 240 LLDAAAQACRAGVKRSHIVSYTEDGALLSELFTRTGNGTLVAQEQFEQLREAGIEDVGGL 299
            L A  QAC  GV R+H+VS  +DGAL+ EL+TR G+GT+V ++ +E +R A IEDV G+
Sbjct: 247 SLRACYQACDGGVSRAHVVSACDDGALIKELYTRDGSGTMVYRDSYETIRRARIEDVVGI 306

Query: 300 IELIRPLEEQGILVRRSREVLEREIEQFSIVEREGLIIACAALYPIADSEAGELACLAVN 359
           + LI PLE++GILV+RSRE LE EI  F+++E++ LI+ CAALYPIA+SEAGELAC+A++
Sbjct: 307 LNLIEPLEQKGILVKRSREHLETEIGFFTVMEKDNLIVGCAALYPIANSEAGELACVAMH 366

Query: 360 PEYRHGGRGDELLERIEERARGLGLKTLFVLTTRTAHWFRERGFQPSSVERLPAARASLY 419
            EYR  GR  +LL  IE +A  L    LF LTT+TAHWF E+GF+   VE+LP  R +LY
Sbjct: 367 NEYRGDGRAAKLLTHIERQAHKLNFTQLFALTTQTAHWFLEQGFRECDVEQLPGERKALY 426

Query: 420 NFQRNSQVFEKSL 432
           N+QR S+VF K++
Sbjct: 427 NYQRRSKVFVKAV 439


Lambda     K      H
   0.321    0.138    0.398 

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: 468
Number of extensions: 18
Number of successful extensions: 2
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: 432
Length of database: 441
Length adjustment: 32
Effective length of query: 400
Effective length of database: 409
Effective search space:   163600
Effective search space used:   163600
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate WP_015817743.1 TERTU_RS01670 (amino-acid N-acetyltransferase)
to HMM TIGR01890 (argA: amino-acid N-acetyltransferase (EC 2.3.1.1))

# 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/TIGR01890.hmm
# target sequence database:        /tmp/gapView.11138.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01890  [M=429]
Accession:   TIGR01890
Description: N-Ac-Glu-synth: amino-acid N-acetyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.4e-165  536.5   0.1   2.8e-165  536.4   0.1    1.0  1  lcl|NCBI__GCF_000023025.1:WP_015817743.1  TERTU_RS01670 amino-acid N-acety


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000023025.1:WP_015817743.1  TERTU_RS01670 amino-acid N-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  536.4   0.1  2.8e-165  2.8e-165       1     428 [.       8     438 ..       8     439 .. 0.97

  Alignments for each domain:
  == domain 1  score: 536.4 bits;  conditional E-value: 2.8e-165
                                 TIGR01890   1 fvkwlreaaPyinahrdktlvvglggelvedknlgklvadiallhslGvrlvlvhGarpqieerlakrg 69 
                                               +++w+r+++Pyin+hr+kt+vv l+g+ + ++n++++++d++ll+slGvrlv+vhGar qi+e+la  +
  lcl|NCBI__GCF_000023025.1:WP_015817743.1   8 YIQWFRHTSPYINSHRGKTFVVLLPGDCISQDNFPNIINDLTLLSSLGVRLVVVHGARRQIDEQLAVIN 76 
                                               799****************************************************************** PP

                                 TIGR01890  70 rtthyvrGlrvtdeaslelvkeaaGelrlaiearlsmslantpmagsrlsvvsGnfvtarPiGvveGvd 138
                                                +t++++G+r+t    ++ v +a G+ r +iea++s  l+++pm gs+++v  Gnfvta P Gv++G+d
  lcl|NCBI__GCF_000023025.1:WP_015817743.1  77 SETEFHKGVRITTREQMGEVLKAIGHARFTIEAAFSSGLPDSPMYGSKIRVRCGNFVTAMPQGVIDGID 145
                                               ********************************************************************* PP

                                 TIGR01890 139 yehtGevrkidaegirrlldersivllsPlgfsvtGeifnlamedvatsvaiklkadklillteedGil 207
                                                + tG+vr +da gir +ld++s+ l+sPlg+s tGe+fnl+  dva  +a +l+adkli    +  i 
  lcl|NCBI__GCF_000023025.1:WP_015817743.1 146 HQLTGKVRSVDASGIRAMLDQNSLALVSPLGYSLTGEAFNLSFADVAIAIANALRADKLIAYNDDGPIT 214
                                               ********************************************************************* PP

                                 TIGR01890 208 dadGklvaelsaqeveslv.erleeet..tarllsaavkalrgGvarshlvsyaedGallqelftrdGi 273
                                               d++G+  +el+  + e+ + e+ ++++  t   l+a  +a+ gGv+r+h+vs   dGal++el+trdG 
  lcl|NCBI__GCF_000023025.1:WP_015817743.1 215 DSQGEQFRELTLLQCERFLlEKQQHNRsnTYFSLRACYQACDGGVSRAHVVSACDDGALIKELYTRDGS 283
                                               **************9997525555555434555899********************************* PP

                                 TIGR01890 274 GtlvskealesireatiddvggilelirPleeqGilvrrsrellereieefsviekdGliigcaalypy 342
                                               Gt+v ++++e+ir+a i+dv gil+li+Ple++Gilv+rsre le ei  f+v+ekd li+gcaalyp+
  lcl|NCBI__GCF_000023025.1:WP_015817743.1 284 GTMVYRDSYETIRRARIEDVVGILNLIEPLEQKGILVKRSREHLETEIGFFTVMEKDNLIVGCAALYPI 352
                                               ********************************************************************* PP

                                 TIGR01890 343 aeeevgelaclavsPeardggrGerllkhiedrarqvGlkrlfvlttrtehWfrerGfaeasvdelPea 411
                                               a++e+gelac+a++ e+r+ gr  +ll+hie +a+++ + +lf+ltt+t+hWf+e+Gf e++v++lP +
  lcl|NCBI__GCF_000023025.1:WP_015817743.1 353 ANSEAGELACVAMHNEYRGDGRAAKLLTHIERQAHKLNFTQLFALTTQTAHWFLEQGFRECDVEQLPGE 421
                                               ********************************************************************* PP

                                 TIGR01890 412 rrklynyqrrskilvkk 428
                                               r+ lynyqrrsk++vk 
  lcl|NCBI__GCF_000023025.1:WP_015817743.1 422 RKALYNYQRRSKVFVKA 438
                                               **************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (441 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: 9.42
//
[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