GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argA in Pseudomonas simiae WCS417

Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate GFF5312 PS417_27195 N-acetylglutamate synthase

Query= BRENDA::P22567
         (432 letters)



>FitnessBrowser__WCS417:GFF5312
          Length = 433

 Score =  744 bits (1920), Expect = 0.0
 Identities = 373/433 (86%), Positives = 402/433 (92%), Gaps = 1/433 (0%)

Query: 1   MPDYVNWLRHASPYINSHRDRTFVVMLPGEGVEHPNFGNIVHDLVLLHSLGARLVLVHGS 60
           MPDYVNWLRHASPYIN+HRD TFVVMLPG+GVEHPNFGNIVHDLVLLHSLG RLVLVHGS
Sbjct: 1   MPDYVNWLRHASPYINAHRDCTFVVMLPGDGVEHPNFGNIVHDLVLLHSLGVRLVLVHGS 60

Query: 61  RPQIEARLAARGLAPRYHRDLRVTDAPTLECVIDAVGSLRIAIEARLSMDMAASPMQGAR 120
           RPQIEARL ARGL P YH  LR+TDA TLECVIDAVG LRIAIEARLSMDMA+SPMQG+R
Sbjct: 61  RPQIEARLEARGLTPAYHEGLRITDAATLECVIDAVGQLRIAIEARLSMDMASSPMQGSR 120

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

Query: 181 NLACEDVAMRAAIDLEAEKLILYGAEQGLLDASGKLVRELRPQQVPAHLQRLGNS-YQAE 239
           NLACEDVA RAAIDL A+KL+L+GA+ GL+D +G+LVRELRPQQVPAHLQRLG+S YQAE
Sbjct: 181 NLACEDVATRAAIDLGADKLLLFGADMGLIDENGRLVRELRPQQVPAHLQRLGSSNYQAE 240

Query: 240 LLDAAAQACRAGVKRSHIVSYTEDGALLSELFTRTGNGTLVAQEQFEQLREAGIEDVGGL 299
           LLDAAA+ACR GV RSHIVSY EDGALL+ELFTR G GTLVAQEQFE +REA IEDVGGL
Sbjct: 241 LLDAAAEACRGGVGRSHIVSYAEDGALLTELFTRDGGGTLVAQEQFELVREAAIEDVGGL 300

Query: 300 IELIRPLEEQGILVRRSREVLEREIEQFSIVEREGLIIACAALYPIADSEAGELACLAVN 359
           ++LI PLEEQGILVRRSREVLEREIEQFS+VEREG+IIACAALY IADS AGELACLAVN
Sbjct: 301 LDLISPLEEQGILVRRSREVLEREIEQFSVVEREGMIIACAALYQIADSNAGELACLAVN 360

Query: 360 PEYRHGGRGDELLERIEERARGLGLKTLFVLTTRTAHWFRERGFQPSSVERLPAARASLY 419
           PEYRHG RGD LLERIE RAR  GLKTLFVLTTRTAHWFRERGF+PSSV+RLP+ARASLY
Sbjct: 361 PEYRHGARGDVLLERIESRARAQGLKTLFVLTTRTAHWFRERGFEPSSVDRLPSARASLY 420

Query: 420 NFQRNSQVFEKSL 432
           N+QRNS++FEK+L
Sbjct: 421 NYQRNSKIFEKAL 433


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: 739
Number of extensions: 14
Number of successful extensions: 2
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: 433
Length adjustment: 32
Effective length of query: 400
Effective length of database: 401
Effective search space:   160400
Effective search space used:   160400
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 GFF5312 PS417_27195 (N-acetylglutamate synthase)
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.32686.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.7e-220  718.3   0.1   1.8e-220  718.2   0.1    1.0  1  lcl|FitnessBrowser__WCS417:GFF5312  PS417_27195 N-acetylglutamate sy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF5312  PS417_27195 N-acetylglutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  718.2   0.1  1.8e-220  1.8e-220       1     429 []       4     433 .]       4     433 .] 0.99

  Alignments for each domain:
  == domain 1  score: 718.2 bits;  conditional E-value: 1.8e-220
                           TIGR01890   1 fvkwlreaaPyinahrdktlvvglggelvedknlgklvadiallhslGvrlvlvhGarpqieerlakrgrtthyv 75 
                                         +v+wlr+a+Pyinahrd+t+vv+l+g++ve++n+g++v+d++llhslGvrlvlvhG+rpqie rl++rg+t+ y+
  lcl|FitnessBrowser__WCS417:GFF5312   4 YVNWLRHASPYINAHRDCTFVVMLPGDGVEHPNFGNIVHDLVLLHSLGVRLVLVHGSRPQIEARLEARGLTPAYH 78 
                                         8************************************************************************** PP

                           TIGR01890  76 rGlrvtdeaslelvkeaaGelrlaiearlsmslantpmagsrlsvvsGnfvtarPiGvveGvdyehtGevrkida 150
                                         +Glr+td+a+le+v++a+G+lr aiearlsm++a++pm+gsrl+v+sGn+vtarPiGv+eGvdy+htGevr++d+
  lcl|FitnessBrowser__WCS417:GFF5312  79 EGLRITDAATLECVIDAVGQLRIAIEARLSMDMASSPMQGSRLRVASGNLVTARPIGVLEGVDYHHTGEVRRVDR 153
                                         *************************************************************************** PP

                           TIGR01890 151 egirrlldersivllsPlgfsvtGeifnlamedvatsvaiklkadklillteedGildadGklvaelsaqevesl 225
                                         +gi+rlldersivllsPlg+s+tGeifnla+edvat++ai+l+adkl+l++++ G++d++G+lv+el++q+v ++
  lcl|FitnessBrowser__WCS417:GFF5312 154 KGINRLLDERSIVLLSPLGYSPTGEIFNLACEDVATRAAIDLGADKLLLFGADMGLIDENGRLVRELRPQQVPAH 228
                                         *************************************************************************** PP

                           TIGR01890 226 verleeet.tarllsaavkalrgGvarshlvsyaedGallqelftrdGiGtlvskealesireatiddvggilel 299
                                         ++rl++   +a+ll+aa++a+rgGv rsh+vsyaedGall+elftrdG Gtlv++e++e +rea i+dvgg+l+l
  lcl|FitnessBrowser__WCS417:GFF5312 229 LQRLGSSNyQAELLDAAAEACRGGVGRSHIVSYAEDGALLTELFTRDGGGTLVAQEQFELVREAAIEDVGGLLDL 303
                                         ****97544****************************************************************** PP

                           TIGR01890 300 irPleeqGilvrrsrellereieefsviekdGliigcaalypyaeeevgelaclavsPeardggrGerllkhied 374
                                         i+PleeqGilvrrsre+lereie+fsv+e++G+ii+caaly +a++++gelaclav+Pe+r+g rG+ ll++ie+
  lcl|FitnessBrowser__WCS417:GFF5312 304 ISPLEEQGILVRRSREVLEREIEQFSVVEREGMIIACAALYQIADSNAGELACLAVNPEYRHGARGDVLLERIES 378
                                         *************************************************************************** PP

                           TIGR01890 375 rarqvGlkrlfvlttrtehWfrerGfaeasvdelPearrklynyqrrskilvkkl 429
                                         rar+ Glk+lfvlttrt+hWfrerGf+++svd+lP ar++lynyqr+ski++k l
  lcl|FitnessBrowser__WCS417:GFF5312 379 RARAQGLKTLFVLTTRTAHWFRERGFEPSSVDRLPSARASLYNYQRNSKIFEKAL 433
                                         ***************************************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (433 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: 00:00:00.02
# Mc/sec: 6.53
//
[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