Alignments for a candidate for argA in Herbaspirillum autotrophicum IAM 14942

GapMind for Amino acid biosynthesis

Alignments for a candidate for argA in Herbaspirillum autotrophicum IAM 14942

Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate WP_050465655.1 AKL27_RS25180 amino-acid N-acetyltransferase

Query= BRENDA::P22567
         (432 letters)



>NCBI__GCF_001189915.1:WP_050465655.1
          Length = 436

 Score =  413 bits (1062), Expect = e-120
 Identities = 222/432 (51%), Positives = 284/432 (65%), Gaps = 3/432 (0%)

Query: 3   DYVNWLRHASPYINSHRDRTFVVMLPGEGVEHPNFGNIVHDLVLLHSLGARLVLVHGSRP 62
           D+V WLR  +PY+++ R +TFVV  PGE V   +   +  DL LLH+LG R+V+VHGSRP
Sbjct: 6   DFVAWLRSVAPYVHAFRGKTFVVAFPGELVTAGDLPVLAQDLSLLHALGIRIVVVHGSRP 65

Query: 63  QIEARLAARGLAPRYHRDLRVTDAPTLECVIDAVGSLRIAIEARLSMDMAASPMQGARLR 122
           Q+E +LA R +  R+H  LR+TD   LEC  +A G LR+ IEA  S  +  +PM  A +R
Sbjct: 66  QVEEQLALRNVEARFHNGLRITDTAALECAKEAAGELRLDIEAAFSQGLPNTPMAHAAIR 125

Query: 123 VAGGNLVTARPIGVVEGVDYHHTGEVRRIDRKGIGRLLDERSIVLLSPLGYSPTGEIFNL 182
           V  GN VTARP+GV++G D   TG VR+I    I  +L+   IVLLSPLG+SPTGE FNL
Sbjct: 126 VISGNFVTARPMGVIDGADLQLTGIVRKIAADAIQPILNAGGIVLLSPLGFSPTGEAFNL 185

Query: 183 ACEDVAMRAAIDLEAEKLILYGAEQGLL-DASGKLVRELRPQQVPAHLQ-RLGNSYQAEL 240
           A EDVA+ AAI L AEKLI +  E GL+ DA G  +REL   Q  A L         A  
Sbjct: 186 AMEDVAVSAAIALRAEKLI-FLTETGLMHDAGGTDIRELSSHQAEAVLSANFLPPDSAFY 244

Query: 241 LDAAAQACRAGVKRSHIVSYTEDGALLSELFTRTGNGTLVAQEQFEQLREAGIEDVGGLI 300
           L +  +AC AGV R+HIV +  DG++L ELFT  G GT++  E  E LREA IEDVGG++
Sbjct: 245 LKSTIKACNAGVSRAHIVPFATDGSVLLELFTHDGIGTMITYENLESLREATIEDVGGIL 304

Query: 301 ELIRPLEEQGILVRRSREVLEREIEQFSIVEREGLIIACAALYPIADSEAGELACLAVNP 360
           +LI PLE  G LV+R RE++EREI  FS++E + +I  CAALYP      GE+ACL VNP
Sbjct: 305 KLIEPLEADGTLVKRGRELIEREIHYFSVIEHDNVIFGCAALYPFPKERMGEMACLTVNP 364

Query: 361 EYRHGGRGDELLERIEERARGLGLKTLFVLTTRTAHWFRERGFQPSSVERLPAARASLYN 420
           E +  G G+ +L+ IE RAR  GL  LFVLTTRT+HWF  RGF P++V+ LP  R  +YN
Sbjct: 365 EVQAQGDGERILKHIEARARESGLTRLFVLTTRTSHWFLRRGFVPATVDDLPKDRQHMYN 424

Query: 421 FQRNSQVFEKSL 432
           +QR S V  K+L
Sbjct: 425 WQRKSLVLIKNL 436


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: 491
Number of extensions: 12
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: 436
Length adjustment: 32
Effective length of query: 400
Effective length of database: 404
Effective search space:   161600
Effective search space used:   161600
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_050465655.1 AKL27_RS25180 (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.4038556.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     5e-192  624.5   0.0   5.6e-192  624.3   0.0    1.0  1  NCBI__GCF_001189915.1:WP_050465655.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001189915.1:WP_050465655.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  624.3   0.0  5.6e-192  5.6e-192       1     429 []       7     436 .]       7     436 .] 0.98

  Alignments for each domain:
  == domain 1  score: 624.3 bits;  conditional E-value: 5.6e-192
                             TIGR01890   1 fvkwlreaaPyinahrdktlvvglggelvedknlgklvadiallhslGvrlvlvhGarpqieerlakrgrtth 73 
                                           fv+wlr++aPy++a+r+kt+vv+++gelv ++ l+ l++d++llh+lG+r+v+vhG+rpq+ee+la r+++++
  NCBI__GCF_001189915.1:WP_050465655.1   7 FVAWLRSVAPYVHAFRGKTFVVAFPGELVTAGDLPVLAQDLSLLHALGIRIVVVHGSRPQVEEQLALRNVEAR 79 
                                           8************************************************************************ PP

                             TIGR01890  74 yvrGlrvtdeaslelvkeaaGelrlaiearlsmslantpmagsrlsvvsGnfvtarPiGvveGvdyehtGevr 146
                                           +++Glr+td a+le++keaaGelrl+iea++s+ l+ntpma + ++v+sGnfvtarP+Gv++G d++ tG vr
  NCBI__GCF_001189915.1:WP_050465655.1  80 FHNGLRITDTAALECAKEAAGELRLDIEAAFSQGLPNTPMAHAAIRVISGNFVTARPMGVIDGADLQLTGIVR 152
                                           ************************************************************************* PP

                             TIGR01890 147 kidaegirrlldersivllsPlgfsvtGeifnlamedvatsvaiklkadklillteedGildadGklvaelsa 219
                                           ki a++i+  l+++ ivllsPlgfs+tGe+fnlamedva s+ai+l+a+kli+lte+  + da G+ ++els+
  NCBI__GCF_001189915.1:WP_050465655.1 153 KIAADAIQPILNAGGIVLLSPLGFSPTGEAFNLAMEDVAVSAAIALRAEKLIFLTETGLMHDAGGTDIRELSS 225
                                           *******************************************************99889999********** PP

                             TIGR01890 220 qeveslver..leeettarllsaavkalrgGvarshlvsyaedGallqelftrdGiGtlvskealesireati 290
                                           +++e+++    l  + +a +l++ +ka+++Gv+r+h+v++a+dG++l+elft+dGiGt+++ e+les+reati
  NCBI__GCF_001189915.1:WP_050465655.1 226 HQAEAVLSAnfLPPD-SAFYLKSTIKACNAGVSRAHIVPFATDGSVLLELFTHDGIGTMITYENLESLREATI 297
                                           999998754114444.599****************************************************** PP

                             TIGR01890 291 ddvggilelirPleeqGilvrrsrellereieefsviekdGliigcaalypyaeeevgelaclavsPeardgg 363
                                           +dvggil+li+Ple++G+lv+r rel+erei+ fsvie+d +i+gcaalyp+++e++ge+acl+v+Pe++  g
  NCBI__GCF_001189915.1:WP_050465655.1 298 EDVGGILKLIEPLEADGTLVKRGRELIEREIHYFSVIEHDNVIFGCAALYPFPKERMGEMACLTVNPEVQAQG 370
                                           ************************************************************************* PP

                             TIGR01890 364 rGerllkhiedrarqvGlkrlfvlttrtehWfrerGfaeasvdelPearrklynyqrrskilvkkl 429
                                           +Ger+lkhie+rar+ Gl rlfvlttrt+hWf++rGf++a+vd+lP++r+++yn+qr+s +l+k+l
  NCBI__GCF_001189915.1:WP_050465655.1 371 DGERILKHIEARARESGLTRLFVLTTRTSHWFLRRGFVPATVDDLPKDRQHMYNWQRKSLVLIKNL 436
                                           ***************************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (436 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: 00:00:00.00
# Mc/sec: 18.97
//
[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