Alignments for a candidate for argA in Cupriavidus basilensis 4G11

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.7932.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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.19
//
[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