GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argA in Pseudomonas fluorescens GW456-L13

Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate PfGW456L13_913 N-acetylglutamate synthase (EC 2.3.1.1)

Query= BRENDA::P22567
         (432 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_913
          Length = 432

 Score =  750 bits (1936), Expect = 0.0
 Identities = 373/432 (86%), Positives = 404/432 (93%)

Query: 1   MPDYVNWLRHASPYINSHRDRTFVVMLPGEGVEHPNFGNIVHDLVLLHSLGARLVLVHGS 60
           MP+YVNWLRHASPYIN+HRD TFVVMLPG+GVEHPNFGNIVHDLVLLHSLG RLVLVHGS
Sbjct: 1   MPEYVNWLRHASPYINAHRDCTFVVMLPGDGVEHPNFGNIVHDLVLLHSLGVRLVLVHGS 60

Query: 61  RPQIEARLAARGLAPRYHRDLRVTDAPTLECVIDAVGSLRIAIEARLSMDMAASPMQGAR 120
           RPQIEARLAARGL P YH  +R+TDA TLECVIDAVG LRIAIEARLSMDMA+SPMQG+R
Sbjct: 61  RPQIEARLAARGLTPHYHHGMRITDAATLECVIDAVGQLRIAIEARLSMDMASSPMQGSR 120

Query: 121 LRVAGGNLVTARPIGVVEGVDYHHTGEVRRIDRKGIGRLLDERSIVLLSPLGYSPTGEIF 180
           LRVA GNLVTARPIGV+EGVDYHHTGEVRR+DRKGI RLLDERSIVLLSPLGYSPTGEIF
Sbjct: 121 LRVASGNLVTARPIGVLEGVDYHHTGEVRRVDRKGINRLLDERSIVLLSPLGYSPTGEIF 180

Query: 181 NLACEDVAMRAAIDLEAEKLILYGAEQGLLDASGKLVRELRPQQVPAHLQRLGNSYQAEL 240
           NLACEDVA RAAIDL A+KL+L+GA+ GL+D  G+LVRELRPQQVPAHLQRLG++YQAEL
Sbjct: 181 NLACEDVATRAAIDLGADKLLLFGADLGLIDEHGRLVRELRPQQVPAHLQRLGSNYQAEL 240

Query: 241 LDAAAQACRAGVKRSHIVSYTEDGALLSELFTRTGNGTLVAQEQFEQLREAGIEDVGGLI 300
           LDAAA+ACR GV RSHIVSY EDGALL+ELFTR G GTLVAQEQFE +REA IEDVGGL+
Sbjct: 241 LDAAAEACRGGVARSHIVSYAEDGALLTELFTRDGGGTLVAQEQFEVVREAAIEDVGGLL 300

Query: 301 ELIRPLEEQGILVRRSREVLEREIEQFSIVEREGLIIACAALYPIADSEAGELACLAVNP 360
           +LI PLEEQGILVRRSREVLEREIEQFS+VEREG+IIACAALY IADS+AGELACLAVNP
Sbjct: 301 DLISPLEEQGILVRRSREVLEREIEQFSVVEREGMIIACAALYQIADSDAGELACLAVNP 360

Query: 361 EYRHGGRGDELLERIEERARGLGLKTLFVLTTRTAHWFRERGFQPSSVERLPAARASLYN 420
           EYRHGGRGDELLERIE RAR  GLKTLFVLTTRTAHWFRERGF PSSV+RLP+ARASLYN
Sbjct: 361 EYRHGGRGDELLERIETRARAQGLKTLFVLTTRTAHWFRERGFVPSSVDRLPSARASLYN 420

Query: 421 FQRNSQVFEKSL 432
           +QRNS++FEK+L
Sbjct: 421 YQRNSKIFEKAL 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: 736
Number of extensions: 14
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 PfGW456L13_913 (N-acetylglutamate synthase (EC 2.3.1.1))
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.19326.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-224  730.9   0.2   2.8e-224  730.7   0.2    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_913  N-acetylglutamate synthase (EC 2


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_913  N-acetylglutamate synthase (EC 2.3.1.1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  730.7   0.2  2.8e-224  2.8e-224       1     429 []       4     432 .]       4     432 .] 1.00

  Alignments for each domain:
  == domain 1  score: 730.7 bits;  conditional E-value: 2.8e-224
                                              TIGR01890   1 fvkwlreaaPyinahrdktlvvglggelvedknlgklvadiallhslGvrlvlvhG 56 
                                                            +v+wlr+a+Pyinahrd+t+vv+l+g++ve++n+g++v+d++llhslGvrlvlvhG
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_913   4 YVNWLRHASPYINAHRDCTFVVMLPGDGVEHPNFGNIVHDLVLLHSLGVRLVLVHG 59 
                                                            8******************************************************* PP

                                              TIGR01890  57 arpqieerlakrgrtthyvrGlrvtdeaslelvkeaaGelrlaiearlsmslantp 112
                                                            +rpqie rla+rg+t+hy++G+r+td+a+le+v++a+G+lr aiearlsm++a++p
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_913  60 SRPQIEARLAARGLTPHYHHGMRITDAATLECVIDAVGQLRIAIEARLSMDMASSP 115
                                                            ******************************************************** PP

                                              TIGR01890 113 magsrlsvvsGnfvtarPiGvveGvdyehtGevrkidaegirrlldersivllsPl 168
                                                            m+gsrl+v+sGn+vtarPiGv+eGvdy+htGevr++d++gi+rlldersivllsPl
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_913 116 MQGSRLRVASGNLVTARPIGVLEGVDYHHTGEVRRVDRKGINRLLDERSIVLLSPL 171
                                                            ******************************************************** PP

                                              TIGR01890 169 gfsvtGeifnlamedvatsvaiklkadklillteedGildadGklvaelsaqeves 224
                                                            g+s+tGeifnla+edvat++ai+l+adkl+l++++ G++d++G+lv+el++q+v +
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_913 172 GYSPTGEIFNLACEDVATRAAIDLGADKLLLFGADLGLIDEHGRLVRELRPQQVPA 227
                                                            ******************************************************** PP

                                              TIGR01890 225 lverleeettarllsaavkalrgGvarshlvsyaedGallqelftrdGiGtlvske 280
                                                            +++rl+++++a+ll+aa++a+rgGvarsh+vsyaedGall+elftrdG Gtlv++e
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_913 228 HLQRLGSNYQAELLDAAAEACRGGVARSHIVSYAEDGALLTELFTRDGGGTLVAQE 283
                                                            ******************************************************** PP

                                              TIGR01890 281 alesireatiddvggilelirPleeqGilvrrsrellereieefsviekdGliigc 336
                                                            ++e++rea i+dvgg+l+li+PleeqGilvrrsre+lereie+fsv+e++G+ii+c
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_913 284 QFEVVREAAIEDVGGLLDLISPLEEQGILVRRSREVLEREIEQFSVVEREGMIIAC 339
                                                            ******************************************************** PP

                                              TIGR01890 337 aalypyaeeevgelaclavsPeardggrGerllkhiedrarqvGlkrlfvlttrte 392
                                                            aaly +a++++gelaclav+Pe+r+ggrG++ll++ie+rar+ Glk+lfvlttrt+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_913 340 AALYQIADSDAGELACLAVNPEYRHGGRGDELLERIETRARAQGLKTLFVLTTRTA 395
                                                            ******************************************************** PP

                                              TIGR01890 393 hWfrerGfaeasvdelPearrklynyqrrskilvkkl 429
                                                            hWfrerGf+++svd+lP ar++lynyqr+ski++k l
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_913 396 HWFRERGFVPSSVDRLPSARASLYNYQRNSKIFEKAL 432
                                                            *********************************9976 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.56
//
[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