Alignments for a candidate for OAT in Lacinutrix algicola AKS293

GapMind for Amino acid biosynthesis

Alignments for a candidate for OAT in Lacinutrix algicola AKS293

Align Ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate WP_055436832.1 ASC41_RS11700 ornithine--oxo-acid transaminase

Query= reanno::Cola:Echvi_0577
         (413 letters)



>NCBI__GCF_001418085.1:WP_055436832.1
          Length = 426

 Score =  589 bits (1518), Expect = e-173
 Identities = 285/419 (68%), Positives = 347/419 (82%), Gaps = 12/419 (2%)

Query: 7   SSQQAIELENKHGAHNYHPLPVVLSRGEGVFMWDVEGEKYYDFLSSYSAVNQGHCHPRIL 66
           +SQ+A++LENK+GAHNYHPLPVVLSRGEGV++WDVEG+KYYDFLS+YSAVNQGHCHPRI+
Sbjct: 8   TSQEAMDLENKYGAHNYHPLPVVLSRGEGVYVWDVEGKKYYDFLSAYSAVNQGHCHPRII 67

Query: 67  QTLIDQAGTLTLTSRAFHNDVLGPFEKFLTEYFGYDKVLPMNTGAEGVETAIKIARKWGY 126
           + + +QA TLTLTSRAF+ND+LG FEK+ TE FG+DK+LPMNTGAE VETA+K+ RKW Y
Sbjct: 68  EAMTNQAKTLTLTSRAFYNDMLGKFEKYATETFGFDKLLPMNTGAEAVETALKLCRKWAY 127

Query: 127 EKKGIPENEGTIIVAKNNFHGRTTTVISFSNDETARKNFGPYTPGFVTIPHDDIDALKDV 186
           E KGI ENE  IIV +NNFHGRTTT+ISFSND  ARKNFGPYT GF+ I ++++ AL++ 
Sbjct: 128 EVKGIDENEAEIIVCENNFHGRTTTIISFSNDPVARKNFGPYTKGFIKIEYNNLKALEEA 187

Query: 187 LSQSKNIIGYLVEPIQGEAGVYVPKEGYLKEVAAVCKDHGVLFMADEIQTGIARTGKLLA 246
           LS + NI G+LVEPIQGEAGVYVP EGYL    A+C+ + VLF+ADE+QTGIARTG+LLA
Sbjct: 188 LSSNNNIAGFLVEPIQGEAGVYVPTEGYLAAAKALCEKYNVLFIADEVQTGIARTGRLLA 247

Query: 247 -CDH-----------EGVKPDMLILGKAISGGFYPVSAVLADDHIMEVIQPGQHGSTFGG 294
            C +             VK D+LILGKA+SGG YPVSAVLA++ IM+VI+PG HGSTFGG
Sbjct: 248 TCGNCTCADKHCSGTPEVKADILILGKALSGGAYPVSAVLANNAIMDVIKPGNHGSTFGG 307

Query: 295 NPLGAKVAMTALNVVKDEKLAENADKLGKLFRERIQQLVDKSDLVELVRGKGLLNAIVIN 354
           NP+ A + M AL V+KDE LAENA  LG+LFR  I + ++ S++V  VRGKGLLNAI+IN
Sbjct: 308 NPVAAAIGMAALEVIKDENLAENAQVLGELFRAEIAKFIETSNIVNGVRGKGLLNAILIN 367

Query: 355 DTEDSDTAWRLCLALKENGLLAKPTHGNIIRFAPPLVITEEQLHDCCDIIEKTIQNFKK 413
           DTEDSDTAW +C+AL++NGLLAKPTHGNIIRFAPPLV+T+EQL DC  II KT+  F+K
Sbjct: 368 DTEDSDTAWNICMALRDNGLLAKPTHGNIIRFAPPLVMTKEQLLDCVSIITKTLAQFEK 426


Lambda     K      H
   0.318    0.137    0.407 

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: 617
Number of extensions: 17
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: 413
Length of database: 426
Length adjustment: 32
Effective length of query: 381
Effective length of database: 394
Effective search space:   150114
Effective search space used:   150114
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_055436832.1 ASC41_RS11700 (ornithine--oxo-acid transaminase)
to HMM TIGR01885 (rocD: ornithine--oxo-acid transaminase (EC 2.6.1.13))

# 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/TIGR01885.hmm
# target sequence database:        /tmp/gapView.970503.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01885  [M=402]
Accession:   TIGR01885
Description: Orn_aminotrans: ornithine--oxo-acid transaminase
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-196  639.4   0.1   1.3e-196  639.1   0.1    1.1  1  NCBI__GCF_001418085.1:WP_055436832.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001418085.1:WP_055436832.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  639.1   0.1  1.3e-196  1.3e-196       1     401 [.       9     421 ..       9     422 .. 0.96

  Alignments for each domain:
  == domain 1  score: 639.1 bits;  conditional E-value: 1.3e-196
                             TIGR01885   1 seevieleekygahnyhplpvvlskaeGakvwdvegkryldflsaysavnqGhchpkivkalveqaqkltlss 73 
                                           s+e+++le+kygahnyhplpvvls++eG++vwdvegk+y+dflsaysavnqGhchp+i++a+++qa++ltl+s
  NCBI__GCF_001418085.1:WP_055436832.1   9 SQEAMDLENKYGAHNYHPLPVVLSRGEGVYVWDVEGKKYYDFLSAYSAVNQGHCHPRIIEAMTNQAKTLTLTS 81 
                                           6899********************************************************************* PP

                             TIGR01885  74 rafyndvfgefaeyvtklfGydkvlpmntGaeavetaiklarkWgykkkkipedkalilsaegnfhGrtlavi 146
                                           rafynd++g+f++y t++fG+dk+lpmntGaeaveta+kl+rkW+y++k+i e++a i+++e+nfhGrt ++i
  NCBI__GCF_001418085.1:WP_055436832.1  82 RAFYNDMLGKFEKYATETFGFDKLLPMNTGAEAVETALKLCRKWAYEVKGIDENEAEIIVCENNFHGRTTTII 154
                                           ************************************************************************* PP

                             TIGR01885 147 slstdpesrenfGpyvpnvkkieynnlealeealeeagekvaaflvePiqGeaGvvvpddgylkkvrelckky 219
                                           s s+dp +r+nfGpy++++ kieynnl+aleeal++ ++++a+flvePiqGeaGv vp +gyl  +++lc+ky
  NCBI__GCF_001418085.1:WP_055436832.1 155 SFSNDPVARKNFGPYTKGFIKIEYNNLKALEEALSS-NNNIAGFLVEPIQGEAGVYVPTEGYLAAAKALCEKY 226
                                           ***********************************9.99********************************** PP

                             TIGR01885 220 nvlliadeiqtGiartGkll.......av.ehe.....evkPdivllGkalsgGvyPvsavladkevmltikp 279
                                           nvl+iade+qtGiartG+ll       +  + +     evk di++lGkalsgG yPvsavla++++m +ikp
  NCBI__GCF_001418085.1:WP_055436832.1 227 NVLFIADEVQTGIARTGRLLatcgnctCAdK-HcsgtpEVKADILILGKALSGGAYPVSAVLANNAIMDVIKP 298
                                           *******************944333321222.1355669********************************** PP

                             TIGR01885 280 gehGstygGnPlasavavaalevlkeeklaeraeklGeelreelkkl..kkeivkevrGkGllnaivideska 350
                                           g+hGst+gGnP+a+a+ +aalev+k+e+lae+a+ lGe +r+e+ k   +++iv+ vrGkGllnai i++++ 
  NCBI__GCF_001418085.1:WP_055436832.1 299 GNHGSTFGGNPVAAAIGMAALEVIKDENLAENAQVLGELFRAEIAKFieTSNIVNGVRGKGLLNAILINDTE- 370
                                           *********************************************9876779******************99. PP

                             TIGR01885 351 ngreawdlclklkekGllakptheeiirlaPPlviteeelkeaveiikkvl 401
                                           ++ +aw++c+ l+++Gllakpth++iir+aPPlv+t+e+l ++v+ii+k+l
  NCBI__GCF_001418085.1:WP_055436832.1 371 DSDTAWNICMALRDNGLLAKPTHGNIIRFAPPLVMTKEQLLDCVSIITKTL 421
                                           9***********************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (402 nodes)
Target sequences:                          1  (426 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: 22.66
//
[ok]

This GapMind analysis is from Jul 26 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 2024 update 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 original 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