Alignments for a candidate for argA in Dechlorosoma suillum PS

GapMind for Amino acid biosynthesis

Alignments for a candidate for argA in Dechlorosoma suillum PS

Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate Dsui_1570 Dsui_1570 amino-acid N-acetyltransferase

Query= BRENDA::P22567
         (432 letters)



>FitnessBrowser__PS:Dsui_1570
          Length = 448

 Score =  413 bits (1062), Expect = e-120
 Identities = 222/436 (50%), Positives = 290/436 (66%), Gaps = 8/436 (1%)

Query: 4   YVNWLRHASPYINSHRDRTFVVMLPGEGVEHPNFGNIVHDLVLLHSLGARLVLVHGSRPQ 63
           +V W R  +PY+N+ R +TFVV   G+ +  P      +D+ LL +LG RLVLVHGSRPQ
Sbjct: 12  FVAWFRSVAPYVNAFRGKTFVVAFGGKSISGPLARTFAYDVSLLANLGVRLVLVHGSRPQ 71

Query: 64  IEARLAARGLAPRYHRDLRVTDAPTLECVIDAVGSLRIAIEARLSMDMAASPMQGARLRV 123
           IE  L  +GL  R+H   R+TDA TL+CVIDAVGS+ + +EA LS  +  +PM G  +RV
Sbjct: 72  IEEELQEKGLESRFHAGQRITDADTLDCVIDAVGSVYLEVEALLSQGLPNTPMAGNTIRV 131

Query: 124 AGGNLVTARPIGVVEGVDYHHTGEVRRIDRKGIGRLLDERSIVLLSPLGYSPTGEIFNLA 183
            GGN +TARP+GV++GVD  +TG VR+ID +G+   L   +IVLLS LG SPTGEIFNL+
Sbjct: 132 VGGNFITARPMGVLDGVDLQYTGAVRKIDAEGLKAQLGLGNIVLLSNLGASPTGEIFNLS 191

Query: 184 CEDVAMRAAIDLEAEKLILYGAEQGLLDASGKLVRELRPQQVPAHLQRLGNSYQAEL--- 240
            E+VA  AA  L A+KLI     QG  DA G L+ EL        L R+G     +L   
Sbjct: 192 MEEVAEEAAKALGADKLIFLTDSQGATDAEGNLLDEL-TADAAEQLARVGEWLSPDLKRY 250

Query: 241 LDAAAQACRAGVKRSHIVSYTEDGALLSELFTRTGNGTLVAQEQFEQLREAGIEDVGGLI 300
           L  A +A R GV R HI+ Y  DGA+L ELFT  G GT+V ++  + LR+A  +D+GGL+
Sbjct: 251 LPCAVRASRRGVGRVHIIGYELDGAVLHELFTHDGVGTVVTRDPLDTLRDAKPDDIGGLV 310

Query: 301 ELIRPLEEQGILVRRSREVLEREIEQFSIVEREGLIIACAALYPIAD----SEAGELACL 356
            LI PLEE G LV R RE+LEREI +FS+VE +G+I+ CAALYP A+    ++  ELACL
Sbjct: 311 GLIAPLEEDGTLVHRPRELLEREIGRFSVVEHDGVIVGCAALYPYAEDGQKAKTAELACL 370

Query: 357 AVNPEYRHGGRGDELLERIEERARGLGLKTLFVLTTRTAHWFRERGFQPSSVERLPAARA 416
           AV+PE+R  G G+ L++ IE +A+  G+K LFVLTTRT HWF ERGF  +SV+ LP  + 
Sbjct: 371 AVSPEHRRWGYGERLMQHIEGKAKAAGVKRLFVLTTRTTHWFIERGFALASVDELPEEKR 430

Query: 417 SLYNFQRNSQVFEKSL 432
            +YN QR S+V  KSL
Sbjct: 431 HMYNLQRRSKVLMKSL 446


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: 553
Number of extensions: 24
Number of successful extensions: 3
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: 448
Length adjustment: 32
Effective length of query: 400
Effective length of database: 416
Effective search space:   166400
Effective search space used:   166400
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 Dsui_1570 Dsui_1570 (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.15028.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.5e-180  585.9   0.0   2.8e-180  585.7   0.0    1.0  1  lcl|FitnessBrowser__PS:Dsui_1570  Dsui_1570 amino-acid N-acetyltra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_1570  Dsui_1570 amino-acid N-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  585.7   0.0  2.8e-180  2.8e-180       1     429 []      12     446 ..      12     446 .. 0.97

  Alignments for each domain:
  == domain 1  score: 585.7 bits;  conditional E-value: 2.8e-180
                         TIGR01890   1 fvkwlreaaPyinahrdktlvvglggelvedknlgklvadiallhslGvrlvlvhGarpqieerlakrgrtthyvrG 77 
                                       fv+w+r++aPy+na+r+kt+vv++gg+ + ++    ++ d++ll +lGvrlvlvhG+rpqiee+l+++g++++++ G
  lcl|FitnessBrowser__PS:Dsui_1570  12 FVAWFRSVAPYVNAFRGKTFVVAFGGKSISGPLARTFAYDVSLLANLGVRLVLVHGSRPQIEEELQEKGLESRFHAG 88 
                                       8**************************************************************************** PP

                         TIGR01890  78 lrvtdeaslelvkeaaGelrlaiearlsmslantpmagsrlsvvsGnfvtarPiGvveGvdyehtGevrkidaegir 154
                                        r+td+ +l++v++a+G++ l++ea ls+ l+ntpmag  ++vv Gnf+tarP+Gv++Gvd+++tG vrkidaeg++
  lcl|FitnessBrowser__PS:Dsui_1570  89 QRITDADTLDCVIDAVGSVYLEVEALLSQGLPNTPMAGNTIRVVGGNFITARPMGVLDGVDLQYTGAVRKIDAEGLK 165
                                       ***************************************************************************** PP

                         TIGR01890 155 rlldersivllsPlgfsvtGeifnlamedvatsvaiklkadklillteedGildadGklvaelsaqeveslverlee 231
                                        +l  ++ivlls lg s+tGeifnl+me+va ++a +l+adkli+lt ++G  da+G+l  el+a+ +e+l+ r++e
  lcl|FitnessBrowser__PS:Dsui_1570 166 AQLGLGNIVLLSNLGASPTGEIFNLSMEEVAEEAAKALGADKLIFLTDSQGATDAEGNLLDELTADAAEQLA-RVGE 241
                                       ****************************************************************76666554.4554 PP

                         TIGR01890 232 et...tarllsaavkalrgGvarshlvsyaedGallqelftrdGiGtlvskealesireatiddvggilelirPlee 305
                                             +r+l  av+a r Gv r+h++ y  dGa+l+elft+dG+Gt v+++ l+++r+a+ dd+gg++ li Plee
  lcl|FitnessBrowser__PS:Dsui_1570 242 WLspdLKRYLPCAVRASRRGVGRVHIIGYELDGAVLHELFTHDGVGTVVTRDPLDTLRDAKPDDIGGLVGLIAPLEE 318
                                       4444469********************************************************************** PP

                         TIGR01890 306 qGilvrrsrellereieefsviekdGliigcaalypyae....eevgelaclavsPeardggrGerllkhiedrarq 378
                                       +G+lv+r rellerei +fsv+e+dG+i+gcaalypyae    ++++elaclavsPe r  g+Gerl++hie +a++
  lcl|FitnessBrowser__PS:Dsui_1570 319 DGTLVHRPRELLEREIGRFSVVEHDGVIVGCAALYPYAEdgqkAKTAELACLAVSPEHRRWGYGERLMQHIEGKAKA 395
                                       *************************************983322478******************************* PP

                         TIGR01890 379 vGlkrlfvlttrtehWfrerGfaeasvdelPearrklynyqrrskilvkkl 429
                                        G+krlfvlttrt+hWf erGfa asvdelPe++r++yn qrrsk+l+k l
  lcl|FitnessBrowser__PS:Dsui_1570 396 AGVKRLFVLTTRTTHWFIERGFALASVDELPEEKRHMYNLQRRSKVLMKSL 446
                                       ************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (448 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: 10.29
//
[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