Alignments for a candidate for OAT in Beijerinckia mobilis UQM 1969

GapMind for Amino acid biosynthesis

Alignments for a candidate for OAT in Beijerinckia mobilis UQM 1969

Align Ornithine aminotransferase; OAT; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 (characterized)
to candidate WP_034992943.1 DL88_RS04220 ornithine--oxo-acid transaminase

Query= SwissProt::P38021
         (401 letters)



>NCBI__GCF_000745425.1:WP_034992943.1
          Length = 414

 Score =  411 bits (1057), Expect = e-119
 Identities = 204/394 (51%), Positives = 268/394 (68%), Gaps = 3/394 (0%)

Query: 8   KEIIDQTSHYGANNYHPLPIVISEALGAWVKDPEGNEYMDMLSAYSAVNQGHRHPKIIQA 67
           +++I     YGA+NY PLP+V++   GA + D EG  Y+DM+SAYSA + GH HP+++ A
Sbjct: 2   QDVIGLEERYGAHNYAPLPVVLTHGRGACLFDEEGRRYIDMMSAYSAASFGHLHPRLVAA 61

Query: 68  LKDQADKITLTSRAFHNDQLGPFYEKTAKLTGKEMILPMNTGAEAVESAVKAARRWAYEV 127
           LK Q D++ L SRAFH D LGPF E  A LTG +  LPMNTGAEAVE+A+KAARR+ Y+ 
Sbjct: 62  LKRQLDRVDLVSRAFHTDGLGPFCEDLAGLTGLDACLPMNTGAEAVETAIKAARRYGYDR 121

Query: 128 KGVADNQAEIIACVGNFHGRTMLAVSLSSEEEYKRGFGPMLPGIKLIPYGDVEALRQAIT 187
             +  ++AEII   GNFHGRT   +  SS+   +RGFGP  PG  ++P+GD  AL  A+ 
Sbjct: 122 LSIPHDKAEIIVAAGNFHGRTTTIIGFSSDAATRRGFGPFAPGFVMVPFGDTGALEAAVG 181

Query: 188 PNTAAFLFEPIQGEAGIVIPPEGFLQEAAAICKEENVLFIADEIQTGLGRTGKTFACDWD 247
           P TAA L EPIQGEAGIV+PP G+L     +C    +L I DEIQ+G GRTG+TFA + +
Sbjct: 182 PCTAAVLIEPIQGEAGIVLPPPGYLSAVRRLCDRHGILLILDEIQSGFGRTGRTFAFEHE 241

Query: 248 GIVPDMYILGKALGGGVFPISCIAADREILGVFNPGSHGSTFGGNPLACAVSIASLEVLE 307
              PD  ILGKALGGG+ P+S   A R ++ VF+PGSHGSTFGGNPLA AV+  ++ VL 
Sbjct: 242 DAKPDGIILGKALGGGLLPVSAFVARRALMDVFDPGSHGSTFGGNPLAMAVAREAMRVLR 301

Query: 308 DEKLADRSLELGEYFKSELESIDSPVIKEVRGRGLFIGVELTEA---ARPYCERLKEEGL 364
           +EKL +RS  LG      L +ID P I+ VRG+GL+ GV+L  A   A+  C ++ E G+
Sbjct: 302 EEKLPERSARLGTILLDALRAIDHPAIRAVRGKGLWAGVDLDPALINAKDVCMKMLEGGV 361

Query: 365 LCKETHDTVIRFAPPLIISKEDLDWAIEKIKHVL 398
           L KETH T IRFAPPL+I+++DL  A+   +  L
Sbjct: 362 LTKETHATTIRFAPPLVIAEDDLLAAVRVFREAL 395


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: 460
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: 401
Length of database: 414
Length adjustment: 31
Effective length of query: 370
Effective length of database: 383
Effective search space:   141710
Effective search space used:   141710
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_034992943.1 DL88_RS04220 (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.12280.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-150  487.9   0.0   1.1e-150  487.7   0.0    1.0  1  lcl|NCBI__GCF_000745425.1:WP_034992943.1  DL88_RS04220 ornithine--oxo-acid


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000745425.1:WP_034992943.1  DL88_RS04220 ornithine--oxo-acid transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  487.7   0.0  1.1e-150  1.1e-150       2     401 ..       2     395 ..       1     396 [. 0.99

  Alignments for each domain:
  == domain 1  score: 487.7 bits;  conditional E-value: 1.1e-150
                                 TIGR01885   2 eevieleekygahnyhplpvvlskaeGakvwdvegkryldflsaysavnqGhchpkivkalveqaqklt 70 
                                               ++vi lee+ygahny plpvvl++++Ga ++d eg+ry+d++saysa + Gh hp++v+al+ q +++ 
  lcl|NCBI__GCF_000745425.1:WP_034992943.1   2 QDVIGLEERYGAHNYAPLPVVLTHGRGACLFDEEGRRYIDMMSAYSAASFGHLHPRLVAALKRQLDRVD 70 
                                               68999**************************************************************** PP

                                 TIGR01885  71 lssrafyndvfgefaeyvtklfGydkvlpmntGaeavetaiklarkWgykkkkipedkalilsaegnfh 139
                                               l sraf++d +g f e ++ l G d +lpmntGaeavetaik ar++gy++  ip+dka i++a+gnfh
  lcl|NCBI__GCF_000745425.1:WP_034992943.1  71 LVSRAFHTDGLGPFCEDLAGLTGLDACLPMNTGAEAVETAIKAARRYGYDRLSIPHDKAEIIVAAGNFH 139
                                               ********************************************************************* PP

                                 TIGR01885 140 GrtlavislstdpesrenfGpyvpnvkkieynnlealeealeeagekvaaflvePiqGeaGvvvpddgy 208
                                               Grt ++i  s+d  +r++fGp++p++  ++++++ ale a+    +  aa+l+ePiqGeaG+v+p  gy
  lcl|NCBI__GCF_000745425.1:WP_034992943.1 140 GRTTTIIGFSSDAATRRGFGPFAPGFVMVPFGDTGALEAAVG---PCTAAVLIEPIQGEAGIVLPPPGY 205
                                               **************************************9875...699********************* PP

                                 TIGR01885 209 lkkvrelckkynvlliadeiqtGiartGkllaveheevkPdivllGkalsgGvyPvsavladkevmlti 277
                                               l  vr lc+++ +lli deiq G +rtG+ +a+ehe+ kPd ++lGkal+gG++Pvsa +a++++m ++
  lcl|NCBI__GCF_000745425.1:WP_034992943.1 206 LSAVRRLCDRHGILLILDEIQSGFGRTGRTFAFEHEDAKPDGIILGKALGGGLLPVSAFVARRALMDVF 274
                                               ********************************************************************* PP

                                 TIGR01885 278 kpgehGstygGnPlasavavaalevlkeeklaeraeklGeelreelkklkkeivkevrGkGllnaivid 346
                                               +pg+hGst+gGnPla ava +a++vl+eekl er+++lG++l ++l+++ ++ ++ vrGkGl +++ +d
  lcl|NCBI__GCF_000745425.1:WP_034992943.1 275 DPGSHGSTFGGNPLAMAVAREAMRVLREEKLPERSARLGTILLDALRAIDHPAIRAVRGKGLWAGVDLD 343
                                               ********************************************************************* PP

                                 TIGR01885 347 eskangreawdlclklkekGllakptheeiirlaPPlviteeelkeaveiikkvl 401
                                               +      +a d+c+k+ e G+l+k+th + ir+aPPlvi+e++l +av++++++l
  lcl|NCBI__GCF_000745425.1:WP_034992943.1 344 PAL---INAKDVCMKMLEGGVLTKETHATTIRFAPPLVIAEDDLLAAVRVFREAL 395
                                               **9...7899*****************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (402 nodes)
Target sequences:                          1  (414 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.26
//
[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