GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argA in Shewanella loihica PV-4

Align amino-acid acetyltransferase (characterized)
to candidate 5211062 Shew_3478 N-acetylglutamate synthase (RefSeq)

Query= CharProtDB::CH_024150
         (443 letters)



>FitnessBrowser__PV4:5211062
          Length = 440

 Score =  584 bits (1506), Expect = e-171
 Identities = 280/438 (63%), Positives = 351/438 (80%)

Query: 5   RKTELVEGFRHSVPYINTHRGKTFVIMLGGEAIEHENFSSIVNDIGLLHSLGIRLVVVYG 64
           R TELVEGFRHS  Y+N HRGKTFV+MLGGEA+    F SI+NDI LLHSLGI++V+V+G
Sbjct: 2   RTTELVEGFRHSASYVNAHRGKTFVVMLGGEALAQSQFRSIINDIALLHSLGIKIVLVHG 61

Query: 65  ARPQIDANLAAHHHEPLYHKNIRVTDAKTLELVKQAAGTLQLDITARLSMSLNNTPLQGA 124
           ARPQID  LAAH+  P Y+  +R++D ++  ++KQ  G LQLDITARLSMSL+NTP+QGA
Sbjct: 62  ARPQIDEALAAHNLAPEYYNGVRISDEESFRVIKQVVGGLQLDITARLSMSLSNTPMQGA 121

Query: 125 HINVVSGNFIIAQPLGVDDGVDYCHSGRIRRIDEDAIHRQLDSGAIVLMGPVAVSVTGES 184
            INVVSGNF+IAQPLGVD+GVDYC SG++RRID   + RQLD+  IVL+GPVA SVTGE 
Sbjct: 122 QINVVSGNFVIAQPLGVDNGVDYCLSGKVRRIDVAGLRRQLDNHGIVLLGPVAASVTGEC 181

Query: 185 FNLTSEEIATQLAIKLKAEKMIGFCSSQGVTNDDGDIVSELFPNEAQARVEAQEEKGDYN 244
           FNLT+EE+ATQ+A+KLKA+KMIGF + +G+ + +G++++EL P +AQ  +    ++ ++ 
Sbjct: 182 FNLTAEEVATQIAVKLKADKMIGFSAKEGILDSNGEVIAELMPTDAQRILSELTDEDNWC 241

Query: 245 SGTVRFLRGAVKACRSGVRRCHLISYQEDGALLQELFSRDGIGTQIVMESAEQIRRATIN 304
            GT  FL+ ++ ACR+GV RCH +SY +DGALLQELFSRDGIGTQIV ESAE++RRATI 
Sbjct: 242 VGTRAFLQASIDACRNGVARCHFVSYLDDGALLQELFSRDGIGTQIVTESAERLRRATIA 301

Query: 305 DIGGILELIRPLEQQGILVRRSREQLEMEIDKFTIIQRDNTTIACAALYPFPEEKIGEMA 364
           DIGG+L+LIRPLEQ G+LVRRSREQLEMEI++F +I+RD   I CAALYPF E+  GE A
Sbjct: 302 DIGGVLDLIRPLEQAGVLVRRSREQLEMEIEQFMLIERDGLVIGCAALYPFEEDNAGEFA 361

Query: 365 CVAVHPDYRSSSRGEVLLERIAAQAKQSGLSKLFVLTTRSIHWFQERGFTPVDIDLLPES 424
           C+ VHPDYR + RG +LL+ I  QAK  G ++LF LTTRSIHWF E GF  V++D LP  
Sbjct: 362 CLVVHPDYRDADRGSILLKNIIGQAKVRGYARLFALTTRSIHWFLEHGFQIVEVDALPNK 421

Query: 425 KKQLYNYQRKSKVLMADL 442
           KKQLYNYQRKSK+L  DL
Sbjct: 422 KKQLYNYQRKSKILALDL 439


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: 594
Number of extensions: 12
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: 443
Length of database: 440
Length adjustment: 32
Effective length of query: 411
Effective length of database: 408
Effective search space:   167688
Effective search space used:   167688
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 5211062 Shew_3478 (N-acetylglutamate synthase (RefSeq))
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.19234.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   1.1e-191  623.3   1.2   1.2e-191  623.2   1.2    1.0  1  lcl|FitnessBrowser__PV4:5211062  Shew_3478 N-acetylglutamate synt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5211062  Shew_3478 N-acetylglutamate synthase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  623.2   1.2  1.2e-191  1.2e-191       1     428 [.       6     438 ..       6     439 .. 0.99

  Alignments for each domain:
  == domain 1  score: 623.2 bits;  conditional E-value: 1.2e-191
                        TIGR01890   1 fvkwlreaaPyinahrdktlvvglggelvedknlgklvadiallhslGvrlvlvhGarpqieerlakrgrtthyvrGl 78 
                                      +v+++r++a y+nahr+kt+vv+lgge+++++++  +++diallhslG+++vlvhGarpqi+e la++++ ++y +G+
  lcl|FitnessBrowser__PV4:5211062   6 LVEGFRHSASYVNAHRGKTFVVMLGGEALAQSQFRSIINDIALLHSLGIKIVLVHGARPQIDEALAAHNLAPEYYNGV 83 
                                      699*************************************************************************** PP

                        TIGR01890  79 rvtdeaslelvkeaaGelrlaiearlsmslantpmagsrlsvvsGnfvtarPiGvveGvdyehtGevrkidaegirrl 156
                                      r+ de s+ ++k+++G l+l+i+arlsmsl+ntpm+g++++vvsGnfv+a+P+Gv++Gvdy+ +G+vr+id++g+rr+
  lcl|FitnessBrowser__PV4:5211062  84 RISDEESFRVIKQVVGGLQLDITARLSMSLSNTPMQGAQINVVSGNFVIAQPLGVDNGVDYCLSGKVRRIDVAGLRRQ 161
                                      ****************************************************************************** PP

                        TIGR01890 157 ldersivllsPlgfsvtGeifnlamedvatsvaiklkadklillteedGildadGklvaelsaqeveslverleeet. 233
                                      ld+  ivll+P++ svtGe+fnl++e+vat++a+klkadk+i +++++Gild++G+++ael++ ++++ + +l +e  
  lcl|FitnessBrowser__PV4:5211062 162 LDNHGIVLLGPVAASVTGECFNLTAEEVATQIAVKLKADKMIGFSAKEGILDSNGEVIAELMPTDAQRILSELTDEDn 239
                                      *************************************************************************99988 PP

                        TIGR01890 234 ....tarllsaavkalrgGvarshlvsyaedGallqelftrdGiGtlvskealesireatiddvggilelirPleeqG 307
                                          t+ +l+a ++a+r Gvar+h+vsy  dGallqelf+rdGiGt++++e++e +r+ati d+gg+l+lirPle+ G
  lcl|FitnessBrowser__PV4:5211062 240 wcvgTRAFLQASIDACRNGVARCHFVSYLDDGALLQELFSRDGIGTQIVTESAERLRRATIADIGGVLDLIRPLEQAG 317
                                      99**************************************************************************** PP

                        TIGR01890 308 ilvrrsrellereieefsviekdGliigcaalypyaeeevgelaclavsPeardggrGerllkhiedrarqvGlkrlf 385
                                      +lvrrsre+le eie+f +ie+dGl+igcaalyp+ e+++ge+acl v+P++rd++rG  llk+i+ +a+  G  rlf
  lcl|FitnessBrowser__PV4:5211062 318 VLVRRSREQLEMEIEQFMLIERDGLVIGCAALYPFEEDNAGEFACLVVHPDYRDADRGSILLKNIIGQAKVRGYARLF 395
                                      ****************************************************************************** PP

                        TIGR01890 386 vlttrtehWfrerGfaeasvdelPearrklynyqrrskilvkk 428
                                      +lttr+ hWf+e+Gf+ ++vd+lP+++++lynyqr+skil   
  lcl|FitnessBrowser__PV4:5211062 396 ALTTRSIHWFLEHGFQIVEVDALPNKKKQLYNYQRKSKILALD 438
                                      ***************************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (440 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: 7.49
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Links

Downloads

Related tools

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