GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argA in Cupriavidus basilensis 4G11

Align amino-acid acetyltransferase (characterized)
to candidate RR42_RS13035 RR42_RS13035 amino acid acetyltransferase

Query= CharProtDB::CH_024150
         (443 letters)



>FitnessBrowser__Cup4G11:RR42_RS13035
          Length = 478

 Score =  389 bits (998), Expect = e-112
 Identities = 197/435 (45%), Positives = 283/435 (65%), Gaps = 4/435 (0%)

Query: 8   ELVEGFRHSVPYINTHRGKTFVIMLGGEAIEHENFSSIVNDIGLLHSLGIRLVVVYGARP 67
           + V+  R   PYI+  RGKTFVI  GGE ++     ++VND+ LLH++G+++V+V+G+RP
Sbjct: 48  QFVDWLRAVAPYIHAFRGKTFVIAFGGELVKANILDALVNDVALLHAMGMQIVLVHGSRP 107

Query: 68  QIDANLAAHHHEPLYHKNIRVTDAKTLELVKQAAGTLQLDITARLSMSLNNTPLQGAHIN 127
           Q++  LA  H E  +   +RVTD   LE  K+AAG L+LDI A  S  L NTP+ GA ++
Sbjct: 108 QVEEQLALRHVESQFADGVRVTDNAALECAKEAAGELRLDIEAAFSQGLPNTPMAGAQLS 167

Query: 128 VVSGNFIIAQPLGVDDGVDYCHSGRIRRIDEDAIHRQLDSGAIVLMGPVAVSVTGESFNL 187
           V+SGNF+ A+PLG+ DGVDY H+G +R+ID +++   L  G IVL+ P+  S TG++FNL
Sbjct: 168 VISGNFVTARPLGIVDGVDYQHTGLVRKIDGESVRMSLSHGKIVLLSPLGFSPTGQAFNL 227

Query: 188 TSEEIATQLAIKLKAEKMIGFCSSQGVTNDDGDIVSELFPNEAQARVEAQEEKGDYNSGT 247
           + E++A+  AI LKA+K++      GV +  G ++ E+    A  R++      D +   
Sbjct: 228 SMEDVASATAIALKADKLVFITEVPGVQDPVGKLMPEMSLRTAIERLQNNHLPPDVS--- 284

Query: 248 VRFLRGAVKACRSGVRRCHLISYQEDGALLQELFSRDGIGTQIVMESAEQIRRATINDIG 307
             +L   VKA + GV R HLI +Q DG++L ELF  DG+GT I     E +R AT++D+G
Sbjct: 285 -YYLEHLVKALKGGVPRAHLIPFQLDGSVLLELFLHDGVGTMISDTDLESLREATLDDVG 343

Query: 308 GILELIRPLEQQGILVRRSREQLEMEIDKFTIIQRDNTTIACAALYPFPEEKIGEMACVA 367
           GIL+LI PLEQ G LV R R  +E +I  F++I+ D     CAALY +P E + EMAC+ 
Sbjct: 344 GILQLIAPLEQDGTLVPRGRHLIERDIANFSVIEHDGVLFGCAALYAYPREGMAEMACLT 403

Query: 368 VHPDYRSSSRGEVLLERIAAQAKQSGLSKLFVLTTRSIHWFQERGFTPVDIDLLPESKKQ 427
           V  + + +  GE LL+RI  +A+  GL +LFVLTTR+ HWF +RGF   ++D LPE K++
Sbjct: 404 VSSEAQGTGDGERLLKRIERRARSLGLDRLFVLTTRTEHWFLKRGFVHANVDDLPEDKRK 463

Query: 428 LYNYQRKSKVLMADL 442
           LYN+QRKS VLM  L
Sbjct: 464 LYNWQRKSMVLMKKL 478


Lambda     K      H
   0.319    0.136    0.384 

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: 502
Number of extensions: 18
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: 443
Length of database: 478
Length adjustment: 33
Effective length of query: 410
Effective length of database: 445
Effective search space:   182450
Effective search space used:   182450
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 RR42_RS13035 RR42_RS13035 (amino acid 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.3288706.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.1e-207  674.2   0.0   4.7e-207  674.0   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS13035  RR42_RS13035 amino acid acetyltr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS13035  RR42_RS13035 amino acid acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  674.0   0.0  4.7e-207  4.7e-207       1     429 []      49     478 .]      49     478 .] 0.99

  Alignments for each domain:
  == domain 1  score: 674.0 bits;  conditional E-value: 4.7e-207
                                 TIGR01890   1 fvkwlreaaPyinahrdktlvvglggelvedknlgklvadiallhslGvrlvlvhGarpqieerlakrg 69 
                                               fv+wlr++aPyi+a+r+kt+v+++ggelv+++ l++lv+d+allh++G+++vlvhG+rpq+ee+la r+
  lcl|FitnessBrowser__Cup4G11:RR42_RS13035  49 FVDWLRAVAPYIHAFRGKTFVIAFGGELVKANILDALVNDVALLHAMGMQIVLVHGSRPQVEEQLALRH 117
                                               8******************************************************************** PP

                                 TIGR01890  70 rtthyvrGlrvtdeaslelvkeaaGelrlaiearlsmslantpmagsrlsvvsGnfvtarPiGvveGvd 138
                                               +++++ +G+rvtd+a+le++keaaGelrl+iea++s+ l+ntpmag++lsv+sGnfvtarP+G+v+Gvd
  lcl|FitnessBrowser__Cup4G11:RR42_RS13035 118 VESQFADGVRVTDNAALECAKEAAGELRLDIEAAFSQGLPNTPMAGAQLSVISGNFVTARPLGIVDGVD 186
                                               ********************************************************************* PP

                                 TIGR01890 139 yehtGevrkidaegirrlldersivllsPlgfsvtGeifnlamedvatsvaiklkadklillteedGil 207
                                               y+htG vrkid e++r +l++++ivllsPlgfs+tG++fnl+medva+ +ai+lkadkl+++te++G+ 
  lcl|FitnessBrowser__Cup4G11:RR42_RS13035 187 YQHTGLVRKIDGESVRMSLSHGKIVLLSPLGFSPTGQAFNLSMEDVASATAIALKADKLVFITEVPGVQ 255
                                               ********************************************************************* PP

                                 TIGR01890 208 dadGklvaelsaqeveslverleeet....tarllsaavkalrgGvarshlvsyaedGallqelftrdG 272
                                               d++Gkl+ e+s   +++++erl+++      +++l++ vkal+gGv+r+hl++++ dG++l+elf++dG
  lcl|FitnessBrowser__Cup4G11:RR42_RS13035 256 DPVGKLMPEMS---LRTAIERLQNNHlppdVSYYLEHLVKALKGGVPRAHLIPFQLDGSVLLELFLHDG 321
                                               **********9...888999999988888889************************************* PP

                                 TIGR01890 273 iGtlvskealesireatiddvggilelirPleeqGilvrrsrellereieefsviekdGliigcaalyp 341
                                               +Gt++s ++les+reat+ddvggil+li Ple++G+lv+r r+l+er+i++fsvie+dG+++gcaaly+
  lcl|FitnessBrowser__Cup4G11:RR42_RS13035 322 VGTMISDTDLESLREATLDDVGGILQLIAPLEQDGTLVPRGRHLIERDIANFSVIEHDGVLFGCAALYA 390
                                               ********************************************************************* PP

                                 TIGR01890 342 yaeeevgelaclavsPeardggrGerllkhiedrarqvGlkrlfvlttrtehWfrerGfaeasvdelPe 410
                                               y+ e+++e+acl+vs ea+++g+Gerllk+ie rar++Gl rlfvlttrtehWf++rGf++a+vd+lPe
  lcl|FitnessBrowser__Cup4G11:RR42_RS13035 391 YPREGMAEMACLTVSSEAQGTGDGERLLKRIERRARSLGLDRLFVLTTRTEHWFLKRGFVHANVDDLPE 459
                                               ********************************************************************* PP

                                 TIGR01890 411 arrklynyqrrskilvkkl 429
                                               ++rklyn+qr+s++l+kkl
  lcl|FitnessBrowser__Cup4G11:RR42_RS13035 460 DKRKLYNWQRKSMVLMKKL 478
                                               *****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (478 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: 11.20
//
[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