Alignments for a candidate for argA in Marinobacter adhaerens HP15

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.16336.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 8.39
//
[ok]

This GapMind analysis is from Apr 09 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