Alignments for a candidate for argA in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for argA in Herbaspirillum seropedicae SmR1

Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate HSERO_RS17320 HSERO_RS17320 amino acid acetyltransferase

Query= BRENDA::P22567
         (432 letters)



>FitnessBrowser__HerbieS:HSERO_RS17320
          Length = 440

 Score =  410 bits (1055), Expect = e-119
 Identities = 218/431 (50%), Positives = 280/431 (64%), Gaps = 1/431 (0%)

Query: 3   DYVNWLRHASPYINSHRDRTFVVMLPGEGVEHPNFGNIVHDLVLLHSLGARLVLVHGSRP 62
           ++VNWLR  +PY+++ R +TFVV  PGE V   +   +  DL LLH+LG R+V+VHGSRP
Sbjct: 9   EFVNWLRSVAPYVHAFRGKTFVVAFPGELVTAGDLQVLAQDLSLLHALGIRVVVVHGSRP 68

Query: 63  QIEARLAARGLAPRYHRDLRVTDAPTLECVIDAVGSLRIAIEARLSMDMAASPMQGARLR 122
           Q+  +LA R +  R+H  LRV D+  LEC  +A G LR+ IEA  S  +  +PM  + +R
Sbjct: 69  QVAEQLALRNVEARFHNGLRVADSAALECAKEAAGELRLDIEAAFSQGLPNTPMAHSAIR 128

Query: 123 VAGGNLVTARPIGVVEGVDYHHTGEVRRIDRKGIGRLLDERSIVLLSPLGYSPTGEIFNL 182
           V  GN VTARP+GV++GVD   TG VR+I    I  +++   IVLLSPLG+SPTGE FNL
Sbjct: 129 VISGNFVTARPMGVIDGVDLQLTGVVRKIAADVIQPIMNAGGIVLLSPLGFSPTGEAFNL 188

Query: 183 ACEDVAMRAAIDLEAEKLILYGAEQGLLDASGKLVRELRPQQVPAHLQRLGNSYQAEL-L 241
             EDVA+ AAI L AEKLI       + DA G  +REL   Q  A L     S +A   L
Sbjct: 189 TMEDVAVSAAIALRAEKLIFLSETPMMTDAGGAEIRELSSHQAEAVLSAGFLSPEAAFYL 248

Query: 242 DAAAQACRAGVKRSHIVSYTEDGALLSELFTRTGNGTLVAQEQFEQLREAGIEDVGGLIE 301
            +  +AC AGV R+HIV +  DG+ L ELFT  G GT+V  E  E LR+A IEDVGG+++
Sbjct: 249 ASVVKACNAGVSRAHIVPFATDGSALLELFTHDGVGTMVTYENLESLRQATIEDVGGILK 308

Query: 302 LIRPLEEQGILVRRSREVLEREIEQFSIVEREGLIIACAALYPIADSEAGELACLAVNPE 361
           LI PLE  G LV+R RE++EREI  FS++E + +I  CAALYP      GE+ACL VNPE
Sbjct: 309 LIEPLEADGTLVKRGRELIEREIHYFSVIEHDNVIFGCAALYPFPKERMGEMACLTVNPE 368

Query: 362 YRHGGRGDELLERIEERARGLGLKTLFVLTTRTAHWFRERGFQPSSVERLPAARASLYNF 421
            +  G GD +L+ IE RAR  GL  LFVLTTRT+HWF +RGF  + V  LP  R  +YN+
Sbjct: 369 VQGQGDGDRILKHIETRAREAGLTKLFVLTTRTSHWFLKRGFVLAGVNDLPQDRQQIYNW 428

Query: 422 QRNSQVFEKSL 432
           QR SQV  K+L
Sbjct: 429 QRKSQVLIKNL 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: 471
Number of extensions: 15
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: 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 HSERO_RS17320 HSERO_RS17320 (amino acid 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.14972.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   2.8e-190  618.7   0.1   3.2e-190  618.5   0.1    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS17320  HSERO_RS17320 amino acid acetylt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS17320  HSERO_RS17320 amino acid acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  618.5   0.1  3.2e-190  3.2e-190       1     429 []      10     439 ..      10     439 .. 0.98

  Alignments for each domain:
  == domain 1  score: 618.5 bits;  conditional E-value: 3.2e-190
                                  TIGR01890   1 fvkwlreaaPyinahrdktlvvglggelvedknlgklvadiallhslGvrlvlvhGarpqieerlakr 68 
                                                fv+wlr++aPy++a+r+kt+vv+++gelv ++ l+ l++d++llh+lG+r+v+vhG+rpq+ e+la r
  lcl|FitnessBrowser__HerbieS:HSERO_RS17320  10 FVNWLRSVAPYVHAFRGKTFVVAFPGELVTAGDLQVLAQDLSLLHALGIRVVVVHGSRPQVAEQLALR 77 
                                                8******************************************************************* PP

                                  TIGR01890  69 grtthyvrGlrvtdeaslelvkeaaGelrlaiearlsmslantpmagsrlsvvsGnfvtarPiGvveG 136
                                                ++++++++Glrv+d a+le++keaaGelrl+iea++s+ l+ntpma s ++v+sGnfvtarP+Gv++G
  lcl|FitnessBrowser__HerbieS:HSERO_RS17320  78 NVEARFHNGLRVADSAALECAKEAAGELRLDIEAAFSQGLPNTPMAHSAIRVISGNFVTARPMGVIDG 145
                                                ******************************************************************** PP

                                  TIGR01890 137 vdyehtGevrkidaegirrlldersivllsPlgfsvtGeifnlamedvatsvaiklkadklillteed 204
                                                vd++ tG+vrki a+ i+  ++++ ivllsPlgfs+tGe+fnl+medva s+ai+l+a+kli+l+e++
  lcl|FitnessBrowser__HerbieS:HSERO_RS17320 146 VDLQLTGVVRKIAADVIQPIMNAGGIVLLSPLGFSPTGEAFNLTMEDVAVSAAIALRAEKLIFLSETP 213
                                                ******************************************************************** PP

                                  TIGR01890 205 GildadGklvaelsaqeveslver.leeettarllsaavkalrgGvarshlvsyaedGallqelftrd 271
                                                 + da G  ++els++++e+++     +   a +l ++vka+++Gv+r+h+v++a+dG+ l+elft+d
  lcl|FitnessBrowser__HerbieS:HSERO_RS17320 214 MMTDAGGAEIRELSSHQAEAVLSAgFLSPEAAFYLASVVKACNAGVSRAHIVPFATDGSALLELFTHD 281
                                                ***************999998865333444599*********************************** PP

                                  TIGR01890 272 GiGtlvskealesireatiddvggilelirPleeqGilvrrsrellereieefsviekdGliigcaal 339
                                                G+Gt+v+ e+les+r+ati+dvggil+li+Ple++G+lv+r rel+erei+ fsvie+d +i+gcaal
  lcl|FitnessBrowser__HerbieS:HSERO_RS17320 282 GVGTMVTYENLESLRQATIEDVGGILKLIEPLEADGTLVKRGRELIEREIHYFSVIEHDNVIFGCAAL 349
                                                ******************************************************************** PP

                                  TIGR01890 340 ypyaeeevgelaclavsPeardggrGerllkhiedrarqvGlkrlfvlttrtehWfrerGfaeasvde 407
                                                yp+++e++ge+acl+v+Pe+++ g+G+r+lkhie+rar+ Gl +lfvlttrt+hWf++rGf+ a+v++
  lcl|FitnessBrowser__HerbieS:HSERO_RS17320 350 YPFPKERMGEMACLTVNPEVQGQGDGDRILKHIETRAREAGLTKLFVLTTRTSHWFLKRGFVLAGVND 417
                                                ******************************************************************** PP

                                  TIGR01890 408 lPearrklynyqrrskilvkkl 429
                                                lP++r++ yn+qr+s++l+k+l
  lcl|FitnessBrowser__HerbieS:HSERO_RS17320 418 LPQDRQQIYNWQRKSQVLIKNL 439
                                                *******************987 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: 11.27
//
[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