Alignments for a candidate for argA in Thioalkalivibrio paradoxus ARh 1

GapMind for Amino acid biosynthesis

Alignments for a candidate for argA in Thioalkalivibrio paradoxus ARh 1

Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate WP_006747000.1 THITH_RS14955 amino-acid N-acetyltransferase

Query= BRENDA::P22567
         (432 letters)



>NCBI__GCF_000227685.2:WP_006747000.1
          Length = 440

 Score =  414 bits (1064), Expect = e-120
 Identities = 224/442 (50%), Positives = 293/442 (66%), Gaps = 26/442 (5%)

Query: 5   VNWLRHASPYINSHRDRTFVVMLPGEGVEHPNFGNIVHDLVLLHSLGARLVLVHGSRPQI 64
           ++W R A PYI +HRDRT V+ + GE  +   F  ++ D+  L +LG R+VLVHG+RPQI
Sbjct: 10  LDWFRAAVPYIVAHRDRTMVIAIAGEAAQALEFPTLLRDIAQLQALGTRVVLVHGARPQI 69

Query: 65  EARLAARGLAPRYHRDLRVTDAPTLECVIDAVGSLRIAIEARLSMDMAASPMQGARLRVA 124
           EARL  RGL PRY   LRVTDA  LE V DAVG LR+ IE  LS ++    + GARLRVA
Sbjct: 70  EARLRERGLTPRYAAGLRVTDAAALEAVCDAVGRLRLHIEGLLSRNLGNPGIAGARLRVA 129

Query: 125 GGNLVTARPIGVVEGVDYHHTGEVRRIDRKGIGRLLDERSIVLLSPLGYSPTGEIFNLAC 184
            GN VTARP+GV EGVD+  TGEVRR+D  GI RLLDE  IVLLSPLGYSPTGE+FNL+ 
Sbjct: 130 SGNFVTARPLGVREGVDFQFTGEVRRVDAPGIVRLLDEGQIVLLSPLGYSPTGEVFNLSG 189

Query: 185 EDVAMRAAIDLEAEKLILYGAEQGLLDASGKLVRELR--------------PQQVPAHLQ 230
           EDVA + A+ L+A+KL+       L D   +++ +L               P+++ AHL+
Sbjct: 190 EDVATQVAVALKADKLVFLTEAGPLRDRQREMLTQLTVSAAERLLTTDSGLPEELAAHLR 249

Query: 231 RLGNSYQAELLDAAAQACRAGVKRSHIVSYTEDGALLSELFTRTGNGTLVAQEQFEQLRE 290
                       +A   C     R H+V    DG LL ELF+R G GTLV++E  E+LR 
Sbjct: 250 ------------SAVDVCTVHDLRVHLVDRHIDGGLLIELFSRQGIGTLVSREPVERLRA 297

Query: 291 AGIEDVGGLIELIRPLEEQGILVRRSREVLEREIEQFSIVEREGLIIACAALYPIADSEA 350
           A ++DVGG+ +LI+PLE +GILVRRSRE LE EI+ F +++ +GLII  AALY   +++A
Sbjct: 298 ATLDDVGGIFDLIQPLESEGILVRRSREHLELEIDCFRVLDADGLIIGTAALYTFPETKA 357

Query: 351 GELACLAVNPEYRHGGRGDELLERIEERARGLGLKTLFVLTTRTAHWFRERGFQPSSVER 410
            E+ACLA++PEYR GGRGD++LE +E  A   G + +FVLTTRT  WF+ERG++   +  
Sbjct: 358 AEIACLALHPEYRGGGRGDQILEHVETLAWRRGHRQVFVLTTRTQQWFQERGYREGQITD 417

Query: 411 LPAARASLYNFQRNSQVFEKSL 432
           LP AR +LYN  RNS+V  K+L
Sbjct: 418 LPPARQALYNQARNSKVLVKAL 439


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: 551
Number of extensions: 17
Number of successful extensions: 3
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: 440
Length adjustment: 32
Effective length of query: 400
Effective length of database: 408
Effective search space:   163200
Effective search space used:   163200
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 WP_006747000.1 THITH_RS14955 (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.32073.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     1e-166  541.1   0.4   1.2e-166  540.8   0.4    1.0  1  lcl|NCBI__GCF_000227685.2:WP_006747000.1  THITH_RS14955 amino-acid N-acety


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000227685.2:WP_006747000.1  THITH_RS14955 amino-acid N-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  540.8   0.4  1.2e-166  1.2e-166       3     429 .]      11     439 ..      10     439 .. 0.98

  Alignments for each domain:
  == domain 1  score: 540.8 bits;  conditional E-value: 1.2e-166
                                 TIGR01890   3 kwlreaaPyinahrdktlvvglggelvedknlgklvadiallhslGvrlvlvhGarpqieerlakrgrt 71 
                                               +w+r+a Pyi ahrd+t+v+++ ge+ ++ +++ l+ dia l++lG r+vlvhGarpqie rl +rg+t
  lcl|NCBI__GCF_000227685.2:WP_006747000.1  11 DWFRAAVPYIVAHRDRTMVIAIAGEAAQALEFPTLLRDIAQLQALGTRVVLVHGARPQIEARLRERGLT 79 
                                               8******************************************************************** PP

                                 TIGR01890  72 thyvrGlrvtdeaslelvkeaaGelrlaiearlsmslantpmagsrlsvvsGnfvtarPiGvveGvdye 140
                                               ++y  Glrvtd+a+le v +a+G+lrl+ie  ls +l n   ag+rl+v+sGnfvtarP+Gv eGvd++
  lcl|NCBI__GCF_000227685.2:WP_006747000.1  80 PRYAAGLRVTDAAALEAVCDAVGRLRLHIEGLLSRNLGNPGIAGARLRVASGNFVTARPLGVREGVDFQ 148
                                               ********************************************************************* PP

                                 TIGR01890 141 htGevrkidaegirrlldersivllsPlgfsvtGeifnlamedvatsvaiklkadklillteedGilda 209
                                               +tGevr++da gi rllde++ivllsPlg+s+tGe+fnl+ edvat+va++lkadkl++lte   + d+
  lcl|NCBI__GCF_000227685.2:WP_006747000.1 149 FTGEVRRVDAPGIVRLLDEGQIVLLSPLGYSPTGEVFNLSGEDVATQVAVALKADKLVFLTEAGPLRDR 217
                                               ********************************************************************* PP

                                 TIGR01890 210 dGklvaelsaqeveslverlee..ettarllsaavkalrgGvarshlvsyaedGallqelftrdGiGtl 276
                                               + ++ ++l+ + +e+l+    +  e  a  l++av+ +     r+hlv+   dG ll elf+r+GiGtl
  lcl|NCBI__GCF_000227685.2:WP_006747000.1 218 QREMLTQLTVSAAERLLTTDSGlpEELAAHLRSAVDVCTVHDLRVHLVDRHIDGGLLIELFSRQGIGTL 286
                                               *************99987643212345999*************************************** PP

                                 TIGR01890 277 vskealesireatiddvggilelirPleeqGilvrrsrellereieefsviekdGliigcaalypyaee 345
                                               vs+e +e +r at+ddvggi++li+Ple +Gilvrrsre le ei+ f v++ dGliig aaly+++e 
  lcl|NCBI__GCF_000227685.2:WP_006747000.1 287 VSREPVERLRAATLDDVGGIFDLIQPLESEGILVRRSREHLELEIDCFRVLDADGLIIGTAALYTFPET 355
                                               ********************************************************************* PP

                                 TIGR01890 346 evgelaclavsPeardggrGerllkhiedrarqvGlkrlfvlttrtehWfrerGfaeasvdelPearrk 414
                                               +++e+acla++Pe+r+ggrG+++l+h+e+ a   G +++fvlttrt++Wf+erG+ e ++ +lP ar+ 
  lcl|NCBI__GCF_000227685.2:WP_006747000.1 356 KAAEIACLALHPEYRGGGRGDQILEHVETLAWRRGHRQVFVLTTRTQQWFQERGYREGQITDLPPARQA 424
                                               ********************************************************************* PP

                                 TIGR01890 415 lynyqrrskilvkkl 429
                                               lyn  r+sk+lvk l
  lcl|NCBI__GCF_000227685.2:WP_006747000.1 425 LYNQARNSKVLVKAL 439
                                               ************976 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: 00:00:00.01
# Mc/sec: 9.47
//
[ok]

This GapMind analysis is from Apr 10 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