GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argA in Pseudomonas stutzeri RCH2

Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate GFF3930 Psest_4000 amino-acid N-acetyltransferase

Query= BRENDA::P22567
         (432 letters)



>FitnessBrowser__psRCH2:GFF3930
          Length = 432

 Score =  751 bits (1940), Expect = 0.0
 Identities = 375/432 (86%), Positives = 405/432 (93%)

Query: 1   MPDYVNWLRHASPYINSHRDRTFVVMLPGEGVEHPNFGNIVHDLVLLHSLGARLVLVHGS 60
           M DYV WLR +SPYINSHRDRTFVVMLPG+G+EH NF NIVHDLVLLHSLG RLVLV GS
Sbjct: 1   MHDYVTWLRDSSPYINSHRDRTFVVMLPGDGLEHANFANIVHDLVLLHSLGVRLVLVFGS 60

Query: 61  RPQIEARLAARGLAPRYHRDLRVTDAPTLECVIDAVGSLRIAIEARLSMDMAASPMQGAR 120
           RPQIEARLAARG+ PR+HRDLRVTDAPT+ECVIDAVG LRIA+EARLSMDMAASPMQGAR
Sbjct: 61  RPQIEARLAARGIEPRFHRDLRVTDAPTMECVIDAVGQLRIALEARLSMDMAASPMQGAR 120

Query: 121 LRVAGGNLVTARPIGVVEGVDYHHTGEVRRIDRKGIGRLLDERSIVLLSPLGYSPTGEIF 180
           LRVAGGN VTARPIGV++GVD HHTGEVRRIDRKGIGRLLDER+IVLLSPLGYSPTGEIF
Sbjct: 121 LRVAGGNFVTARPIGVLDGVDLHHTGEVRRIDRKGIGRLLDERTIVLLSPLGYSPTGEIF 180

Query: 181 NLACEDVAMRAAIDLEAEKLILYGAEQGLLDASGKLVRELRPQQVPAHLQRLGNSYQAEL 240
           NLACEDVA RAAIDL+A+KL+LYGAE GLLD SGKLVRELRPQQ+PA+++RLG+ YQAEL
Sbjct: 181 NLACEDVATRAAIDLQADKLVLYGAEPGLLDESGKLVRELRPQQIPAYVERLGSQYQAEL 240

Query: 241 LDAAAQACRAGVKRSHIVSYTEDGALLSELFTRTGNGTLVAQEQFEQLREAGIEDVGGLI 300
           LDAAAQACR GV+RSH+VSY +DGALL+ELFTR G GTLV QEQFEQLREA IEDVGGLI
Sbjct: 241 LDAAAQACRGGVRRSHVVSYADDGALLNELFTRDGGGTLVTQEQFEQLREATIEDVGGLI 300

Query: 301 ELIRPLEEQGILVRRSREVLEREIEQFSIVEREGLIIACAALYPIADSEAGELACLAVNP 360
           +LI PLEEQGILVRRSREVLERE+EQFSIVER+GLIIACAALYPIADS+AGELACLAVNP
Sbjct: 301 DLITPLEEQGILVRRSREVLEREVEQFSIVERDGLIIACAALYPIADSDAGELACLAVNP 360

Query: 361 EYRHGGRGDELLERIEERARGLGLKTLFVLTTRTAHWFRERGFQPSSVERLPAARASLYN 420
           EYRHGGRGDELLERIEERAR LGLK L VLTTRTAHWFRERGF+P SV+RLPAARASLYN
Sbjct: 361 EYRHGGRGDELLERIEERARKLGLKKLIVLTTRTAHWFRERGFEPISVDRLPAARASLYN 420

Query: 421 FQRNSQVFEKSL 432
           FQRNS++FEK L
Sbjct: 421 FQRNSKIFEKPL 432


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: 744
Number of extensions: 19
Number of successful extensions: 1
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: 432
Length adjustment: 32
Effective length of query: 400
Effective length of database: 400
Effective search space:   160000
Effective search space used:   160000
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 GFF3930 Psest_4000 (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.2933830.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   5.5e-214  696.8   0.0   6.1e-214  696.7   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF3930  Psest_4000 amino-acid N-acetyltr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF3930  Psest_4000 amino-acid N-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  696.7   0.0  6.1e-214  6.1e-214       1     429 []       4     432 .]       4     432 .] 1.00

  Alignments for each domain:
  == domain 1  score: 696.7 bits;  conditional E-value: 6.1e-214
                           TIGR01890   1 fvkwlreaaPyinahrdktlvvglggelvedknlgklvadiallhslGvrlvlvhGarpqieerlakrgrtthyv 75 
                                         +v wlr+++Pyin+hrd+t+vv+l+g+++e+ n++++v+d++llhslGvrlvlv G+rpqie rla+rg++++++
  lcl|FitnessBrowser__psRCH2:GFF3930   4 YVTWLRDSSPYINSHRDRTFVVMLPGDGLEHANFANIVHDLVLLHSLGVRLVLVFGSRPQIEARLAARGIEPRFH 78 
                                         89************************************************************************* PP

                           TIGR01890  76 rGlrvtdeaslelvkeaaGelrlaiearlsmslantpmagsrlsvvsGnfvtarPiGvveGvdyehtGevrkida 150
                                         r lrvtd+ ++e+v++a+G+lr a+earlsm++a++pm+g+rl+v+ GnfvtarPiGv++Gvd++htGevr+id+
  lcl|FitnessBrowser__psRCH2:GFF3930  79 RDLRVTDAPTMECVIDAVGQLRIALEARLSMDMAASPMQGARLRVAGGNFVTARPIGVLDGVDLHHTGEVRRIDR 153
                                         *************************************************************************** PP

                           TIGR01890 151 egirrlldersivllsPlgfsvtGeifnlamedvatsvaiklkadklillteedGildadGklvaelsaqevesl 225
                                         +gi rllder ivllsPlg+s+tGeifnla+edvat++ai+l+adkl+l ++e+G+ld++Gklv+el++q++ + 
  lcl|FitnessBrowser__psRCH2:GFF3930 154 KGIGRLLDERTIVLLSPLGYSPTGEIFNLACEDVATRAAIDLQADKLVLYGAEPGLLDESGKLVRELRPQQIPAY 228
                                         *************************************************************************** PP

                           TIGR01890 226 verleeettarllsaavkalrgGvarshlvsyaedGallqelftrdGiGtlvskealesireatiddvggileli 300
                                         verl+++++a+ll+aa++a+rgGv+rsh+vsya dGall+elftrdG Gtlv++e++e++reati+dvgg+++li
  lcl|FitnessBrowser__psRCH2:GFF3930 229 VERLGSQYQAELLDAAAQACRGGVRRSHVVSYADDGALLNELFTRDGGGTLVTQEQFEQLREATIEDVGGLIDLI 303
                                         *************************************************************************** PP

                           TIGR01890 301 rPleeqGilvrrsrellereieefsviekdGliigcaalypyaeeevgelaclavsPeardggrGerllkhiedr 375
                                          PleeqGilvrrsre+lere+e+fs++e+dGlii+caalyp+a++++gelaclav+Pe+r+ggrG++ll++ie+r
  lcl|FitnessBrowser__psRCH2:GFF3930 304 TPLEEQGILVRRSREVLEREVEQFSIVERDGLIIACAALYPIADSDAGELACLAVNPEYRHGGRGDELLERIEER 378
                                         *************************************************************************** PP

                           TIGR01890 376 arqvGlkrlfvlttrtehWfrerGfaeasvdelPearrklynyqrrskilvkkl 429
                                         ar++Glk+l vlttrt+hWfrerGf++ svd+lP+ar++lyn+qr+ski++k+l
  lcl|FitnessBrowser__psRCH2:GFF3930 379 ARKLGLKKLIVLTTRTAHWFRERGFEPISVDRLPAARASLYNFQRNSKIFEKPL 432
                                         ***************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (432 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: 00:00:00.00
# Mc/sec: 19.42
//
[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