Alignments for a candidate for OAT in Nitriliruptor alkaliphilus DSM 45188

GapMind for Amino acid biosynthesis

Alignments for a candidate for OAT in Nitriliruptor alkaliphilus DSM 45188

Align Ornithine aminotransferase; OAT; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 (characterized)
to candidate WP_052665020.1 NITAL_RS04820 ornithine--oxo-acid transaminase

Query= SwissProt::P38021
         (401 letters)



>NCBI__GCF_000969705.1:WP_052665020.1
          Length = 412

 Score =  408 bits (1049), Expect = e-118
 Identities = 205/373 (54%), Positives = 253/373 (67%), Gaps = 1/373 (0%)

Query: 17  YGANNYHPLPIVISEALGAWVKDPEGNEYMDMLSAYSAVNQGHRHPKIIQALKDQADKIT 76
           + ANNYHPLP+VI+EA G WV D EG  Y+D L+ YSA+N GHRHP +I A   Q D++T
Sbjct: 18  HSANNYHPLPVVIAEAEGTWVTDTEGRRYLDCLAGYSALNFGHRHPDLIAAAHAQLDRVT 77

Query: 77  LTSRAFHNDQLGPFYEKTAKLTGKEMILPMNTGAEAVESAVKAARRWAYEVKGVADNQAE 136
           LTSRAF +D+   F    A+LTG +++LPMNTGAEAVE+A+K ARRW Y VKGVA  QA 
Sbjct: 78  LTSRAFRHDRFADFTAAVARLTGMDVVLPMNTGAEAVETAIKLARRWGYRVKGVAAGQAT 137

Query: 137 IIACVGNFHGRTMLAVSLSSEEEYKRGFGPMLPGIKLIPYGDVEALRQAITPNTAAFLFE 196
           I+    NFHGRT   V  S +      FGP  PG   IP+GD  AL  AI   T A L E
Sbjct: 138 IVVMDSNFHGRTTTIVGFSDDPVAHEDFGPFAPGFVRIPFGDAAALEAAIDDTTVAVLLE 197

Query: 197 PIQGEAGIVIPPEGFLQEAAAICKEENVLFIADEIQTGLGRTGKTFACDWDGIVPDMYIL 256
           PIQGEAGI++PPEG+L+E   I  E  VL IADEIQ+GLGRTG TFACD + +VPD+++L
Sbjct: 198 PIQGEAGIIVPPEGYLREVRRITHERGVLMIADEIQSGLGRTGTTFACDLEDVVPDVFVL 257

Query: 257 GKALGGGVFPISCIAADREILGVFNPGSHGSTFGGNPLACAVSIASLEVLEDEKLADRSL 316
           GKALGGGV P+S +AA RE++ VF PGSHGSTFGGNPLA AV+   + +LE      R  
Sbjct: 258 GKALGGGVVPVSAVAARRELMDVFTPGSHGSTFGGNPLAAAVATEVVRLLETGVYQARGR 317

Query: 317 ELGEYFKSELESIDSPVIKEVRGRGLFIGVEL-TEAARPYCERLKEEGLLCKETHDTVIR 375
           ELG+   + L ++ S  + EVR  GL+ GVEL    AR   E L   G+L K+TH T IR
Sbjct: 318 ELGDRLATRLRALPSSQVAEVRCIGLWAGVELVAPVARAVSEALMTRGVLAKDTHATTIR 377

Query: 376 FAPPLIISKEDLD 388
            APPL I+ E++D
Sbjct: 378 LAPPLTITAEEID 390


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: 450
Number of extensions: 20
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: 401
Length of database: 412
Length adjustment: 31
Effective length of query: 370
Effective length of database: 381
Effective search space:   140970
Effective search space used:   140970
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_052665020.1 NITAL_RS04820 (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.29956.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.7e-138  447.6   0.0   2.2e-138  447.3   0.0    1.0  1  lcl|NCBI__GCF_000969705.1:WP_052665020.1  NITAL_RS04820 ornithine--oxo-aci


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000969705.1:WP_052665020.1  NITAL_RS04820 ornithine--oxo-acid transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  447.3   0.0  2.2e-138  2.2e-138      10     401 ..      17     400 ..      12     401 .. 0.98

  Alignments for each domain:
  == domain 1  score: 447.3 bits;  conditional E-value: 2.2e-138
                                 TIGR01885  10 kygahnyhplpvvlskaeGakvwdvegkryldflsaysavnqGhchpkivkalveqaqkltlssrafyn 78 
                                                ++a+nyhplpvv++ aeG+ v d+eg+ryld l++ysa+n Gh hp++++a   q +++tl+sraf  
  lcl|NCBI__GCF_000969705.1:WP_052665020.1  17 PHSANNYHPLPVVIAEAEGTWVTDTEGRRYLDCLAGYSALNFGHRHPDLIAAAHAQLDRVTLTSRAFRH 85 
                                               589****************************************************************** PP

                                 TIGR01885  79 dvfgefaeyvtklfGydkvlpmntGaeavetaiklarkWgykkkkipedkalilsaegnfhGrtlavis 147
                                               d f++f   v++l G d vlpmntGaeavetaiklar+Wgy++k++++ +a+i++++ nfhGrt +++ 
  lcl|NCBI__GCF_000969705.1:WP_052665020.1  86 DRFADFTAAVARLTGMDVVLPMNTGAEAVETAIKLARRWGYRVKGVAAGQATIVVMDSNFHGRTTTIVG 154
                                               ********************************************************************* PP

                                 TIGR01885 148 lstdpesrenfGpyvpnvkkieynnlealeealeeagekvaaflvePiqGeaGvvvpddgylkkvrelc 216
                                                s dp ++e+fGp++p++ +i++++++ale a+++   + +a+l+ePiqGeaG++vp +gyl++vr + 
  lcl|NCBI__GCF_000969705.1:WP_052665020.1 155 FSDDPVAHEDFGPFAPGFVRIPFGDAAALEAAIDD---TTVAVLLEPIQGEAGIIVPPEGYLREVRRIT 220
                                               *********************************99...77899************************** PP

                                 TIGR01885 217 kkynvlliadeiqtGiartGkllaveheevkPdivllGkalsgGvyPvsavladkevmltikpgehGst 285
                                               ++  vl+iadeiq G++rtG  +a++ e+v Pd+ +lGkal+gGv+Pvsav a++e+m +++pg+hGst
  lcl|NCBI__GCF_000969705.1:WP_052665020.1 221 HERGVLMIADEIQSGLGRTGTTFACDLEDVVPDVFVLGKALGGGVVPVSAVAARRELMDVFTPGSHGST 289
                                               ********************************************************************* PP

                                 TIGR01885 286 ygGnPlasavavaalevlkeeklaeraeklGeelreelkklkkeivkevrGkGllnaivideskangre 354
                                               +gGnPla+ava + +++l+      r ++lG++l ++l++l ++ v evr  Gl +++ +   +     
  lcl|NCBI__GCF_000969705.1:WP_052665020.1 290 FGGNPLAAAVATEVVRLLETGVYQARGRELGDRLATRLRALPSSQVAEVRCIGLWAGVELVAPV----- 353
                                               ***********************************************************99888..... PP

                                 TIGR01885 355 awdlclklkekGllakptheeiirlaPPlviteeelkeaveiikkvl 401
                                               a  +   l+ +G+lak+th + irlaPPl+it ee++   + ++ ++
  lcl|NCBI__GCF_000969705.1:WP_052665020.1 354 ARAVSEALMTRGVLAKDTHATTIRLAPPLTITAEEIDLLADALAAAI 400
                                               6778999*****************************98888877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (402 nodes)
Target sequences:                          1  (412 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: 12.02
//
[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