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

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.30279.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.16
//
[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