Alignments for a candidate for OAT in Desulfotomaculum ruminis DSM 2154

GapMind for Amino acid biosynthesis

Alignments for a candidate for OAT in Desulfotomaculum ruminis DSM 2154

Align Ornithine aminotransferase; OAT; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 (characterized)
to candidate WP_013843687.1 DESRU_RS18845 ornithine--oxo-acid transaminase

Query= SwissProt::P38021
         (401 letters)



>NCBI__GCF_000215085.1:WP_013843687.1
          Length = 396

 Score =  601 bits (1550), Expect = e-176
 Identities = 289/391 (73%), Positives = 332/391 (84%)

Query: 4   LSKSKEIIDQTSHYGANNYHPLPIVISEALGAWVKDPEGNEYMDMLSAYSAVNQGHRHPK 63
           ++ S  II++T   GA NYHPLPIVI++A G WV+DPEGN YMDMLSAYSA+NQGHRHPK
Sbjct: 1   MNLSNNIIEKTEALGARNYHPLPIVIAKAEGVWVEDPEGNRYMDMLSAYSALNQGHRHPK 60

Query: 64  IIQALKDQADKITLTSRAFHNDQLGPFYEKTAKLTGKEMILPMNTGAEAVESAVKAARRW 123
           II+ALKDQADK+TLTSRAFHNDQL  FYEK A++TGK  ILPMNTGAEAVE+AVKA RRW
Sbjct: 61  IIKALKDQADKVTLTSRAFHNDQLYRFYEKLAQVTGKNRILPMNTGAEAVETAVKAIRRW 120

Query: 124 AYEVKGVADNQAEIIACVGNFHGRTMLAVSLSSEEEYKRGFGPMLPGIKLIPYGDVEALR 183
           AY+ K V +NQAEII C GNFHGRT    S SSEEEYKRGFGP  PG K+IPYGD EAL+
Sbjct: 121 AYDRKKVVENQAEIIVCRGNFHGRTTTITSFSSEEEYKRGFGPFTPGFKIIPYGDTEALK 180

Query: 184 QAITPNTAAFLFEPIQGEAGIVIPPEGFLQEAAAICKEENVLFIADEIQTGLGRTGKTFA 243
            AI PNTAAFL EPIQGEAGIVIP EGFLQEA AICKE N+LF+ADEIQTG GRTG+ FA
Sbjct: 181 GAIMPNTAAFLLEPIQGEAGIVIPREGFLQEAYAICKENNLLFVADEIQTGFGRTGRWFA 240

Query: 244 CDWDGIVPDMYILGKALGGGVFPISCIAADREILGVFNPGSHGSTFGGNPLACAVSIASL 303
           CDW+G+VPD+YI+GKALGGGV PIS +AAD +ILGVF PGSHGSTFGGNPLACAV++A+L
Sbjct: 241 CDWEGVVPDIYIMGKALGGGVLPISAVAADEDILGVFEPGSHGSTFGGNPLACAVAVAAL 300

Query: 304 EVLEDEKLADRSLELGEYFKSELESIDSPVIKEVRGRGLFIGVELTEAARPYCERLKEEG 363
           EVLE+E L  +SL LGEYF ++L+ I +PVIKE+RG+GLFIG+EL   ARPYCE+LKE  
Sbjct: 301 EVLEEENLPQQSLTLGEYFMNQLKQIKNPVIKEIRGKGLFIGLELNTEARPYCEKLKEMK 360

Query: 364 LLCKETHDTVIRFAPPLIISKEDLDWAIEKI 394
           LLCKETH   IRFAPPL I++E+LDWA E+I
Sbjct: 361 LLCKETHVHTIRFAPPLTITREELDWAYERI 391


Lambda     K      H
   0.318    0.136    0.401 

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: 585
Number of extensions: 19
Number of successful extensions: 1
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: 401
Length of database: 396
Length adjustment: 31
Effective length of query: 370
Effective length of database: 365
Effective search space:   135050
Effective search space used:   135050
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_013843687.1 DESRU_RS18845 (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.18535.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.2e-160  519.2   0.0   3.6e-160  519.0   0.0    1.0  1  lcl|NCBI__GCF_000215085.1:WP_013843687.1  DESRU_RS18845 ornithine--oxo-aci


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000215085.1:WP_013843687.1  DESRU_RS18845 ornithine--oxo-acid transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  519.0   0.0  3.6e-160  3.6e-160       1     400 [.       4     394 ..       4     396 .] 0.98

  Alignments for each domain:
  == domain 1  score: 519.0 bits;  conditional E-value: 3.6e-160
                                 TIGR01885   1 seevieleekygahnyhplpvvlskaeGakvwdvegkryldflsaysavnqGhchpkivkalveqaqkl 69 
                                               s+++ie+ e  ga+nyhplp+v++kaeG+ v d+eg+ry+d+lsaysa+nqGh hpki+kal++qa+k+
  lcl|NCBI__GCF_000215085.1:WP_013843687.1   4 SNNIIEKTEALGARNYHPLPIVIAKAEGVWVEDPEGNRYMDMLSAYSALNQGHRHPKIIKALKDQADKV 72 
                                               57899999************************************************************* PP

                                 TIGR01885  70 tlssrafyndvfgefaeyvtklfGydkvlpmntGaeavetaiklarkWgykkkkipedkalilsaegnf 138
                                               tl+sraf+nd++ +f e+++++ G +++lpmntGaeaveta+k  r+W+y++kk+ e++a i++++gnf
  lcl|NCBI__GCF_000215085.1:WP_013843687.1  73 TLTSRAFHNDQLYRFYEKLAQVTGKNRILPMNTGAEAVETAVKAIRRWAYDRKKVVENQAEIIVCRGNF 141
                                               ********************************************************************* PP

                                 TIGR01885 139 hGrtlavislstdpesrenfGpyvpnvkkieynnlealeealeeagekvaaflvePiqGeaGvvvpddg 207
                                               hGrt ++ s s+++e +++fGp++p++k i+y+++eal+ a+     + aafl+ePiqGeaG+v+p +g
  lcl|NCBI__GCF_000215085.1:WP_013843687.1 142 HGRTTTITSFSSEEEYKRGFGPFTPGFKIIPYGDTEALKGAIMP---NTAAFLLEPIQGEAGIVIPREG 207
                                               ***************************************99976...9********************* PP

                                 TIGR01885 208 ylkkvrelckkynvlliadeiqtGiartGkllaveheevkPdivllGkalsgGvyPvsavladkevmlt 276
                                               +l++++++ck++n+l++adeiqtG +rtG+ +a+++e+v Pdi ++Gkal+gGv+P+sav ad++++ +
  lcl|NCBI__GCF_000215085.1:WP_013843687.1 208 FLQEAYAICKENNLLFVADEIQTGFGRTGRWFACDWEGVVPDIYIMGKALGGGVLPISAVAADEDILGV 276
                                               ********************************************************************* PP

                                 TIGR01885 277 ikpgehGstygGnPlasavavaalevlkeeklaeraeklGeelreelkklkkeivkevrGkGllnaivi 345
                                               ++pg+hGst+gGnPla+avavaalevl+ee+l +++  lGe + ++lk++k++++ke+rGkGl+ ++ +
  lcl|NCBI__GCF_000215085.1:WP_013843687.1 277 FEPGSHGSTFGGNPLACAVAVAALEVLEEENLPQQSLTLGEYFMNQLKQIKNPVIKEIRGKGLFIGLEL 345
                                               *******************************************************************99 PP

                                 TIGR01885 346 deskangreawdlclklkekGllakptheeiirlaPPlviteeelkeaveiikkv 400
                                               + ++         c klke  ll k+th + ir+aPPl+it+eel++a e i+ +
  lcl|NCBI__GCF_000215085.1:WP_013843687.1 346 NTEA------RPYCEKLKEMKLLCKETHVHTIRFAPPLTITREELDWAYERIAAC 394
                                               9887......678***********************************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (402 nodes)
Target sequences:                          1  (396 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: 8.90
//
[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