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.21249.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 11.05
//
[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:

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