Alignments for a candidate for argA in Thiomicrorhabdus chilensis DSM 12352

GapMind for Amino acid biosynthesis

Alignments for a candidate for argA in Thiomicrorhabdus chilensis DSM 12352

Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate WP_028487019.1 B076_RS0109010 amino-acid N-acetyltransferase

Query= BRENDA::P22567
         (432 letters)



>NCBI__GCF_000483485.1:WP_028487019.1
          Length = 429

 Score =  332 bits (851), Expect = 1e-95
 Identities = 187/431 (43%), Positives = 271/431 (62%), Gaps = 10/431 (2%)

Query: 3   DYVNWLRHASPYINSHRDRTFVVMLPGEGV-EHPNFGNIVHDLVLLHSLGARLVLVHGSR 61
           D++N LR +S YI  HR +T V+ LPGE + +  +   +  D+ LLH+LG +LVLV G+ 
Sbjct: 7   DFINSLRQSSRYIEEHRGKTCVIYLPGELLLKEASRKQLAQDVGLLHNLGLKLVLVMGAT 66

Query: 62  PQIEARLAARGLAPRYHRDLRVTDAPTLECVIDAVGSLRIAIEARLSMDMAASPMQGARL 121
           PQI+A L   G   + H+  R+T    L     A+G+++  +EA  S    A+ MQ   +
Sbjct: 67  PQIDAALKLYGEEWQTHQQFRITTTEMLPVFQQAIGTVKTQLEASFSQ---ANCMQPTPI 123

Query: 122 RVAGGNLVTARPIGVVEGVDYHHTGEVRRIDRKGIGRLLDERSIVLLSPLGYSPTGEIFN 181
            +  GN V A+P GV+EG+DY HTG++R+I+ + I   LD   I LL+PL YS TGE+FN
Sbjct: 124 TITSGNWVIAQPKGVIEGIDYQHTGKLRKINHQAIAANLDAGQIALLTPLAYSLTGEVFN 183

Query: 182 LACEDVAMRAAIDLEAEKLILYGAEQGLLDASGKLVRELRPQQVPAHLQRLGNSYQAELL 241
           L   + A   A  ++A+KL+++     +     +L ++L   ++   L     + Q  LL
Sbjct: 184 LNTLEQACEVASAIKADKLMVFTTPAEMQ----QLPKQLSIPELDGVLLTPSTADQQRLL 239

Query: 242 DAAAQACRAGVKRSHIVSYTEDGALLSELFTRTGNGTLVAQEQFEQLREAGIEDVGGLIE 301
               +  +  VKR H++   +  A+L ELFTR G+GTL+  +++ Q+R+A IEDVGG+++
Sbjct: 240 TQIRKTSQ-NVKRVHLMDKQDPSAILIELFTRDGSGTLIFSDRYHQVRDAQIEDVGGILD 298

Query: 302 LIRPLEEQGILVRRSREVLEREIEQFSIVEREGLIIACAALYPIADSEAGELACLAVNPE 361
           LI PLE+QG+LV+RSRE+LE EI  F ++ER+  II CAALY   +++ GELACLAV+P+
Sbjct: 299 LISPLEQQGVLVKRSRELLELEIGNFIVLERDQHIIGCAALYQ-HENDFGELACLAVHPQ 357

Query: 362 YRHGGRGDELLERIEERARGLGLKTLFVLTTRTAHWFRERGFQPSSVERLPAARASLYNF 421
           Y+    G ELL  +E +A+ L LKTLF+LTT T HWF E GFQ    E+LP  R SLYNF
Sbjct: 358 YQGQELGSELLAAVENKAKALSLKTLFLLTTHTQHWFIEHGFQADEKEKLPEKRQSLYNF 417

Query: 422 QRNSQVFEKSL 432
           QRNS+V  K L
Sbjct: 418 QRNSKVLFKPL 428


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: 459
Number of extensions: 16
Number of successful extensions: 5
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: 429
Length adjustment: 32
Effective length of query: 400
Effective length of database: 397
Effective search space:   158800
Effective search space used:   158800
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_028487019.1 B076_RS0109010 (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.1679468.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.4e-139  448.9   0.1   1.1e-138  448.8   0.1    1.0  1  NCBI__GCF_000483485.1:WP_028487019.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000483485.1:WP_028487019.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  448.8   0.1  1.1e-138  1.1e-138       1     429 []       8     428 ..       8     428 .. 0.96

  Alignments for each domain:
  == domain 1  score: 448.8 bits;  conditional E-value: 1.1e-138
                             TIGR01890   1 fvkwlreaaPyinahrdktlvvglggelv.edknlgklvadiallhslGvrlvlvhGarpqieerlakrgrtt 72 
                                           f++ lr+++ yi++hr+kt v+ l+gel+ ++   ++l++d++llh+lG++lvlv Ga pqi+  l+  g + 
  NCBI__GCF_000483485.1:WP_028487019.1   8 FINSLRQSSRYIEEHRGKTCVIYLPGELLlKEASRKQLAQDVGLLHNLGLKLVLVMGATPQIDAALKLYGEEW 80 
                                           799************************8626777899************************************ PP

                             TIGR01890  73 hyvrGlrvtdeaslelvkeaaGelrlaiearlsmslantpmagsrlsvvsGnfvtarPiGvveGvdyehtGev 145
                                           + ++ +r+t    l + ++a G++++++ea++s++     m+++ +++ sGn+v+a+P Gv+eG+dy+htG++
  NCBI__GCF_000483485.1:WP_028487019.1  81 QTHQQFRITTTEMLPVFQQAIGTVKTQLEASFSQA---NCMQPTPITITSGNWVIAQPKGVIEGIDYQHTGKL 150
                                           *********************************85...78********************************* PP

                             TIGR01890 146 rkidaegirrlldersivllsPlgfsvtGeifnlamedvatsvaiklkadklillteedGildadGklvaels 218
                                           rki+ ++i  +ld+++i ll+Pl++s tGe+fnl++++ a++va ++kadkl+++t+   +     +l ++ls
  NCBI__GCF_000483485.1:WP_028487019.1 151 RKINHQAIAANLDAGQIALLTPLAYSLTGEVFNLNTLEQACEVASAIKADKLMVFTTPAEM----QQLPKQLS 219
                                           *******************************************************997655....46888999 PP

                             TIGR01890 219 aqeveslverleeettarllsaavkalrgGvarshlvsyaedGallqelftrdGiGtlvskealesireatid 291
                                             e++ ++       ++rll+++ k+    v+r+hl++ +   a+l elftrdG Gtl+  + + ++r+a+i+
  NCBI__GCF_000483485.1:WP_028487019.1 220 IPELDGVLLTPSTADQQRLLTQIRKTS-QNVKRVHLMDKQDPSAILIELFTRDGSGTLIFSDRYHQVRDAQIE 291
                                           999999888888888899*99988876.57******************************************* PP

                             TIGR01890 292 dvggilelirPleeqGilvrrsrellereieefsviekdGliigcaalypyaeeevgelaclavsPeardggr 364
                                           dvggil+li+Ple+qG+lv+rsrelle ei +f v+e+d  iigcaaly + e++ gelaclav+P++++ + 
  NCBI__GCF_000483485.1:WP_028487019.1 292 DVGGILDLISPLEQQGVLVKRSRELLELEIGNFIVLERDQHIIGCAALYQH-ENDFGELACLAVHPQYQGQEL 363
                                           *************************************************86.789****************** PP

                             TIGR01890 365 GerllkhiedrarqvGlkrlfvlttrtehWfrerGfaeasvdelPearrklynyqrrskilvkkl 429
                                           G +ll+ +e++a+++ lk+lf ltt+t+hWf e+Gf+  + ++lPe+r++lyn+qr+sk+l k+l
  NCBI__GCF_000483485.1:WP_028487019.1 364 GSELLAAVENKAKALSLKTLFLLTTHTQHWFIEHGFQADEKEKLPEKRQSLYNFQRNSKVLFKPL 428
                                           *************************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (429 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 17.75
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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