GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argA in Marinobacter adhaerens HP15

Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate GFF3372 HP15_3314 N-acetyllutamate synthase

Query= BRENDA::P22567
         (432 letters)



>FitnessBrowser__Marino:GFF3372
          Length = 435

 Score =  476 bits (1226), Expect = e-139
 Identities = 234/431 (54%), Positives = 316/431 (73%), Gaps = 1/431 (0%)

Query: 3   DYVNWLRHASPYINSHRDRTFVVMLPGEGVEHPNFGNIVHDLVLLHSLGARLVLVHGSRP 62
           D+++  RH+SPYIN+HR RT V+ +PG+ +EH NF NI+HD+ LL SLG RLV+  G+RP
Sbjct: 5   DWLHGFRHSSPYINAHRGRTVVLTIPGDAIEHGNFINIIHDIALLSSLGVRLVVAFGARP 64

Query: 63  QIEARLAARGLAPRYHRDLRVTDAPTLECVIDAVGSLRIAIEARLSMDMAASPMQGARLR 122
           QI+ RL A G+   + + LR+T    L  V++AVG LR  +E+ LSM +  SPM  AR+R
Sbjct: 65  QIQTRLDAAGIESSFSKGLRITPQEHLSMVMEAVGGLRAYLESHLSMGLVNSPMHNARIR 124

Query: 123 VAGGNLVTARPIGVVEGVDYHHTGEVRRIDRKGIGRLLDERSIVLLSPLGYSPTGEIFNL 182
           V+GGN V A+P+GV++G+D+ HTG+VRR+D  GI +LL+   IVLL P+GYSPTG+ FNL
Sbjct: 125 VSGGNYVAAKPVGVLDGIDFGHTGKVRRVDVAGIEKLLELGHIVLLPPMGYSPTGDAFNL 184

Query: 183 ACEDVAMRAAIDLEAEKLILYGAEQGLLDASGKLVRELRPQQVPAHLQRLG-NSYQAELL 241
           + EDV  + A  L+AEKL+++  + GL +  G L+REL  +Q    L       + A+LL
Sbjct: 185 SYEDVGSQVAAALQAEKLMVFIDDPGLQEEDGTLIRELSARQASERLAAGAVTGHDADLL 244

Query: 242 DAAAQACRAGVKRSHIVSYTEDGALLSELFTRTGNGTLVAQEQFEQLREAGIEDVGGLIE 301
            AA  AC  GV+R+HI+SY +DGALL ELFTR G GTLV+ + +EQ R+A +ED+GG++E
Sbjct: 245 RAACDACVKGVRRAHIISYVDDGALLKELFTRDGAGTLVSGDHYEQFRQARVEDIGGILE 304

Query: 302 LIRPLEEQGILVRRSREVLEREIEQFSIVEREGLIIACAALYPIADSEAGELACLAVNPE 361
           LI+PLEEQGILVRRSRE+LE EI++F + ER+G I+ CAALY   +  AGEL+C AV+P 
Sbjct: 305 LIQPLEEQGILVRRSREMLETEIDRFVVAERDGTIVGCAALYSYPEEGAGELSCFAVDPT 364

Query: 362 YRHGGRGDELLERIEERARGLGLKTLFVLTTRTAHWFRERGFQPSSVERLPAARASLYNF 421
           YR  GRGDE+L  +E+ ARG G++ LFVLTT+T HWFRERGFQPS+V+ LP  + + YN 
Sbjct: 365 YRRAGRGDEILAMVEKLARGQGIQKLFVLTTQTEHWFRERGFQPSTVQALPGPKLAAYNT 424

Query: 422 QRNSQVFEKSL 432
           QRNS+VF K L
Sbjct: 425 QRNSKVFFKPL 435


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: 558
Number of extensions: 23
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: 435
Length adjustment: 32
Effective length of query: 400
Effective length of database: 403
Effective search space:   161200
Effective search space used:   161200
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 GFF3372 HP15_3314 (N-acetyllutamate synthase)
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.644.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   5.1e-174  565.1   0.0   5.8e-174  565.0   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF3372  HP15_3314 N-acetyllutamate synth


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF3372  HP15_3314 N-acetyllutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  565.0   0.0  5.8e-174  5.8e-174       3     429 .]       8     435 .]       6     435 .] 0.98

  Alignments for each domain:
  == domain 1  score: 565.0 bits;  conditional E-value: 5.8e-174
                           TIGR01890   3 kwlreaaPyinahrdktlvvglggelvedknlgklvadiallhslGvrlvlvhGarpqieerlakrgrtthyvrG 77 
                                         +++r+++Pyinahr++t+v++++g+++e++n+ ++++diall+slGvrlv+  Garpqi+ rl++ g+++ + +G
  lcl|FitnessBrowser__Marino:GFF3372   8 HGFRHSSPYINAHRGRTVVLTIPGDAIEHGNFINIIHDIALLSSLGVRLVVAFGARPQIQTRLDAAGIESSFSKG 82 
                                         68************************************************************************* PP

                           TIGR01890  78 lrvtdeaslelvkeaaGelrlaiearlsmslantpmagsrlsvvsGnfvtarPiGvveGvdyehtGevrkidaeg 152
                                         lr+t +  l +v+ea+G lr  +e++lsm l n+pm  +r++v  Gn+v a+P+Gv++G+d+ htG+vr++d++g
  lcl|FitnessBrowser__Marino:GFF3372  83 LRITPQEHLSMVMEAVGGLRAYLESHLSMGLVNSPMHNARIRVSGGNYVAAKPVGVLDGIDFGHTGKVRRVDVAG 157
                                         *************************************************************************** PP

                           TIGR01890 153 irrlldersivllsPlgfsvtGeifnlamedvatsvaiklkadklillteedGildadGklvaelsaqev.eslv 226
                                         i++ll+ ++ivll+P+g+s+tG++fnl+ edv ++va +l+a+kl+++  ++G+ ++dG+l++elsa+++ e+l+
  lcl|FitnessBrowser__Marino:GFF3372 158 IEKLLELGHIVLLPPMGYSPTGDAFNLSYEDVGSQVAAALQAEKLMVFIDDPGLQEEDGTLIRELSARQAsERLA 232
                                         ******************************************************************988725667 PP

                           TIGR01890 227 erleeettarllsaavkalrgGvarshlvsyaedGallqelftrdGiGtlvskealesireatiddvggilelir 301
                                           +  +  a ll+aa +a+  Gv+r+h++sy  dGall+elftrdG Gtlvs +++e+ r+a ++d+ggileli+
  lcl|FitnessBrowser__Marino:GFF3372 233 AGAVTGHDADLLRAACDACVKGVRRAHIISYVDDGALLKELFTRDGAGTLVSGDHYEQFRQARVEDIGGILELIQ 307
                                         77888889******************************************************************* PP

                           TIGR01890 302 PleeqGilvrrsrellereieefsviekdGliigcaalypyaeeevgelaclavsPeardggrGerllkhiedra 376
                                         PleeqGilvrrsre+le ei++f v e+dG+i+gcaaly+y+ee++gel+c+av+P +r +grG+++l+ +e+ a
  lcl|FitnessBrowser__Marino:GFF3372 308 PLEEQGILVRRSREMLETEIDRFVVAERDGTIVGCAALYSYPEEGAGELSCFAVDPTYRRAGRGDEILAMVEKLA 382
                                         *************************************************************************** PP

                           TIGR01890 377 rqvGlkrlfvlttrtehWfrerGfaeasvdelPearrklynyqrrskilvkkl 429
                                         r+ G+++lfvltt+tehWfrerGf++++v++lP  +   yn qr+sk++ k+l
  lcl|FitnessBrowser__Marino:GFF3372 383 RGQGIQKLFVLTTQTEHWFRERGFQPSTVQALPGPKLAAYNTQRNSKVFFKPL 435
                                         *************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (435 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: 12.08
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Links

Downloads

Related tools

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:

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:

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:

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:

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