Alignments for a candidate for argA in Oleispira antarctica

GapMind for Amino acid biosynthesis

Alignments for a candidate for argA in Oleispira antarctica

Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate WP_046010347.1 OLEAN_RS17770 amino-acid N-acetyltransferase

Query= BRENDA::P22567
         (432 letters)



>NCBI__GCF_000967895.1:WP_046010347.1
          Length = 440

 Score =  447 bits (1150), Expect = e-130
 Identities = 229/436 (52%), Positives = 302/436 (69%), Gaps = 9/436 (2%)

Query: 4   YVNWLRHASPYINSHRDRTFVVMLPGEGVEHPNFGNIVHDLVLLHSLGARLVLVHGSRPQ 63
           YV W RH+SPYIN+HR +TFV+ML G+ +   NF +IV D+ LL+SLG RLV+VHG+RPQ
Sbjct: 6   YVKWFRHSSPYINAHRGKTFVLMLEGDAIADDNFAHIVQDIALLNSLGVRLVIVHGARPQ 65

Query: 64  IEARLAARGLAPRYHRDLRVTDAPTLECVIDAVGSLRIAIEARLSMDMAASPMQGARLRV 123
           I+  L    +  ++H DLR+TD   L  V  A+G ++  IEARLS+ +  +PM GAR+RV
Sbjct: 66  IDQALNVLNIKSQFHGDLRITDQAALNAVRAAIGIVKSDIEARLSVGLPNTPMHGARIRV 125

Query: 124 AGGNLVTARPIGVVEGVDYHHTGEVRRIDRKGIGRLLDERSIVLLSPLGYSPTGEIFNLA 183
             GN VTA+P GV++GVD+ HTGEVRRIDR+ I + LD+ +IVLLS  GYSP+GE+FNLA
Sbjct: 126 VSGNFVTAKPKGVIDGVDFQHTGEVRRIDRQAISQQLDQGNIVLLSSCGYSPSGEMFNLA 185

Query: 184 CEDVAMRAAIDLEAEKLILYGAEQGLL-------DASGKLVRELRPQQVPAHLQRLGNSY 236
            EDVA + AI L AEKLIL G  +GL          S  ++ +L   ++   +  L   +
Sbjct: 186 AEDVATQTAISLTAEKLILMGESEGLPATAKESDSDSSMVISQLTTDELSRIIDSLSGEH 245

Query: 237 QAELLDAAAQACRAGVKRSHIVSYTEDGALLSELFTRTGNGTLVAQEQFEQLREAGIEDV 296
           +   L AA+ A +A + R H++SY  DGALL ELFT  G GTL+  + +E LR+A  EDV
Sbjct: 246 KFHAL-AASTAIKAHINRVHLLSYKVDGALLQELFTHEGAGTLITADDYELLRQATTEDV 304

Query: 297 GGLIELIRPLEEQGILVRRSREVLEREIEQFSIVEREGLIIACAALYPIADSEAGELACL 356
            G++EL+ PLEEQG+LVRRSRE+LE EI +F ++E +G++IACAALYP + S+  ELAC+
Sbjct: 305 AGILELLTPLEEQGVLVRRSRELLETEIHRFKVIELDGMVIACAALYPYS-SDLAELACV 363

Query: 357 AVNPEYRHGGRGDELLERIEERARGLGLKTLFVLTTRTAHWFRERGFQPSSVERLPAARA 416
           AV  EYR G RGD LL  I  +A+   +  LFVLTTRTAHWF ERGF  + +  LP  R 
Sbjct: 364 AVREEYRSGQRGDRLLNAISAQAKAEKINNLFVLTTRTAHWFMERGFSEADISALPQERQ 423

Query: 417 SLYNFQRNSQVFEKSL 432
           SLYNFQRNS++F K L
Sbjct: 424 SLYNFQRNSKIFIKEL 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: 510
Number of extensions: 12
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_046010347.1 OLEAN_RS17770 (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.32298.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.1e-179  582.9   1.8   2.4e-179  582.7   1.8    1.0  1  lcl|NCBI__GCF_000967895.1:WP_046010347.1  OLEAN_RS17770 amino-acid N-acety


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000967895.1:WP_046010347.1  OLEAN_RS17770 amino-acid N-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  582.7   1.8  2.4e-179  2.4e-179       1     429 []       6     439 ..       6     439 .. 0.97

  Alignments for each domain:
  == domain 1  score: 582.7 bits;  conditional E-value: 2.4e-179
                                 TIGR01890   1 fvkwlreaaPyinahrdktlvvglggelvedknlgklvadiallhslGvrlvlvhGarpqieerlakrg 69 
                                               +vkw+r+++Pyinahr+kt+v++l+g++++d+n++++v+diall+slGvrlv+vhGarpqi++ l+  +
  lcl|NCBI__GCF_000967895.1:WP_046010347.1   6 YVKWFRHSSPYINAHRGKTFVLMLEGDAIADDNFAHIVQDIALLNSLGVRLVIVHGARPQIDQALNVLN 74 
                                               8******************************************************************** PP

                                 TIGR01890  70 rtthyvrGlrvtdeaslelvkeaaGelrlaiearlsmslantpmagsrlsvvsGnfvtarPiGvveGvd 138
                                               ++++++  lr+td+a+l+ v+ a G ++++iearls  l+ntpm g+r++vvsGnfvta+P Gv++Gvd
  lcl|NCBI__GCF_000967895.1:WP_046010347.1  75 IKSQFHGDLRITDQAALNAVRAAIGIVKSDIEARLSVGLPNTPMHGARIRVVSGNFVTAKPKGVIDGVD 143
                                               ********************************************************************* PP

                                 TIGR01890 139 yehtGevrkidaegirrlldersivllsPlgfsvtGeifnlamedvatsvaiklkadklillteedGi. 206
                                               ++htGevr+id+++i+++ld+++ivlls  g+s++Ge+fnla+edvat++ai+l a+klil++e++G+ 
  lcl|NCBI__GCF_000967895.1:WP_046010347.1 144 FQHTGEVRRIDRQAISQQLDQGNIVLLSSCGYSPSGEMFNLAAEDVATQTAISLTAEKLILMGESEGLp 212
                                               *******************************************************************94 PP

                                 TIGR01890 207 .....ldadG.klvaelsaqeveslverleeettarllsaavkalrgGvarshlvsyaedGallqelft 269
                                                    +d+d   ++ +l+++e+ + +++l +e + + l aa  a+++ ++r+hl+sy+ dGallqelft
  lcl|NCBI__GCF_000967895.1:WP_046010347.1 213 atakeSDSDSsMVISQLTTDELSRIIDSLSGEHKFHAL-AASTAIKAHINRVHLLSYKVDGALLQELFT 280
                                               4433334444146789****************966665.6789************************** PP

                                 TIGR01890 270 rdGiGtlvskealesireatiddvggilelirPleeqGilvrrsrellereieefsviekdGliigcaa 338
                                               ++G Gtl++ +++e +r+at +dv+gilel+ PleeqG+lvrrsrelle ei++f vie dG++i+caa
  lcl|NCBI__GCF_000967895.1:WP_046010347.1 281 HEGAGTLITADDYELLRQATTEDVAGILELLTPLEEQGVLVRRSRELLETEIHRFKVIELDGMVIACAA 349
                                               ********************************************************************* PP

                                 TIGR01890 339 lypyaeeevgelaclavsPeardggrGerllkhiedrarqvGlkrlfvlttrtehWfrerGfaeasvde 407
                                               lypy+ ++++elac+av  e+r g+rG+rll+ i ++a++  +++lfvlttrt+hWf+erGf+ea++ +
  lcl|NCBI__GCF_000967895.1:WP_046010347.1 350 LYPYS-SDLAELACVAVREEYRSGQRGDRLLNAISAQAKAEKINNLFVLTTRTAHWFMERGFSEADISA 417
                                               ****7.689************************************************************ PP

                                 TIGR01890 408 lPearrklynyqrrskilvkkl 429
                                               lP++r++lyn+qr+ski++k+l
  lcl|NCBI__GCF_000967895.1:WP_046010347.1 418 LPQERQSLYNFQRNSKIFIKEL 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: 9.86
//
[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