Alignments for a candidate for OAT in Sinorhizobium fredii NGR234

GapMind for Amino acid biosynthesis

Alignments for a candidate for OAT in Sinorhizobium fredii NGR234

Align Ornithine aminotransferase; OAT; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 (characterized)
to candidate YP_002827571.1 NGR_c30830 ornithine--oxo-acid transaminase

Query= SwissProt::P38021
         (401 letters)



>NCBI__GCF_000018545.1:YP_002827571.1
          Length = 401

 Score =  440 bits (1131), Expect = e-128
 Identities = 212/397 (53%), Positives = 282/397 (71%), Gaps = 4/397 (1%)

Query: 6   KSKEIIDQTSHY-GANNYHPLPIVISEALGAWVKDPEGNEYMDMLSAYSAVNQGHRHPKI 64
           K+   + +T H  GA+NY PL +V++   G +V D EGN Y+D LSAYSAVNQGH HPKI
Sbjct: 2   KTTAALIETEHLLGAHNYKPLDVVLTRGEGVFVWDIEGNRYLDCLSAYSAVNQGHCHPKI 61

Query: 65  IQALKDQADKITLTSRAFHNDQLGPFYEKTAKLTGKEMILPMNTGAEAVESAVKAARRWA 124
            +A+ +QA K+TLTSRAF NDQL  FYE+ A LTG   +LPMN+GAEAVE+A+KA R+W 
Sbjct: 62  FKAMVEQAQKLTLTSRAFRNDQLALFYEEIAALTGSHKVLPMNSGAEAVETAIKAVRKWG 121

Query: 125 YEVKGVADNQAEIIACVGNFHGRTMLAVSLSSEEEYKRGFGPMLPGIKLIPYGDVEALRQ 184
           YEVKGVA +QAEII C  NFHGRT+  V  S++ +   GFGP  PG +++P+GD++A R 
Sbjct: 122 YEVKGVAADQAEIIVCANNFHGRTIGIVGFSTDPDSHDGFGPFAPGFRIVPFGDIDAFRA 181

Query: 185 AITPNTAAFLFEPIQGEAGIVIPPEGFLQEAAAICKEENVLFIADEIQTGLGRTGKTFAC 244
           AI+ NT AFL EPIQGEAG+++PP G+  E   +C +  +  + DEIQTGLGRTGK  A 
Sbjct: 182 AISENTVAFLVEPIQGEAGVIVPPAGYFAEVRELCTKHAITLVLDEIQTGLGRTGKLLAE 241

Query: 245 DWDGIVPDMYILGKALGGGVFPISCIAADREILGVFNPGSHGSTFGGNPLACAVSIASLE 304
           + + I  D+ ++GKAL GG +P+S + ++ E+LGV  PG HGSTFGGNPLACA++ A+L+
Sbjct: 242 EHEAIEADVTLIGKALSGGFYPVSAVLSNSEVLGVLKPGQHGSTFGGNPLACAIARAALK 301

Query: 305 VLEDEKLADRSLELGEYFKSELESIDSPVIKEVRGRGLFIGVELTE---AARPYCERLKE 361
           VL +E + + S  +GE F + L  I S +I+EVRGRGL + VEL      AR YCE LK 
Sbjct: 302 VLTEEGMIENSARMGERFMTGLTDIRSNIIREVRGRGLMLAVELVPEAGGARKYCEALKA 361

Query: 362 EGLLCKETHDTVIRFAPPLIISKEDLDWAIEKIKHVL 398
            G+L K+TH   IR APPL+I+  ++DWA+E+   VL
Sbjct: 362 RGILAKDTHGDTIRIAPPLVITAGEVDWALEQFAAVL 398


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: 468
Number of extensions: 13
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: 401
Length adjustment: 31
Effective length of query: 370
Effective length of database: 370
Effective search space:   136900
Effective search space used:   136900
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 YP_002827571.1 NGR_c30830 (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.4426.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.9e-169  549.6   0.0   2.2e-169  549.3   0.0    1.0  1  lcl|NCBI__GCF_000018545.1:YP_002827571.1  NGR_c30830 ornithine--oxo-acid t


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000018545.1:YP_002827571.1  NGR_c30830 ornithine--oxo-acid transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  549.3   0.0  2.2e-169  2.2e-169       3     400 ..       6     397 ..       4     399 .. 0.98

  Alignments for each domain:
  == domain 1  score: 549.3 bits;  conditional E-value: 2.2e-169
                                 TIGR01885   3 evieleekygahnyhplpvvlskaeGakvwdvegkryldflsaysavnqGhchpkivkalveqaqkltl 71 
                                               ++ie+e+  gahny+pl+vvl+++eG++vwd+eg+ryld lsaysavnqGhchpki ka+veqaqkltl
  lcl|NCBI__GCF_000018545.1:YP_002827571.1   6 ALIETEHLLGAHNYKPLDVVLTRGEGVFVWDIEGNRYLDCLSAYSAVNQGHCHPKIFKAMVEQAQKLTL 74 
                                               6899***************************************************************** PP

                                 TIGR01885  72 ssrafyndvfgefaeyvtklfGydkvlpmntGaeavetaiklarkWgykkkkipedkalilsaegnfhG 140
                                               +sraf nd+++ f e ++ l G  kvlpmn+Gaeavetaik +rkWgy++k++++d+a i+++++nfhG
  lcl|NCBI__GCF_000018545.1:YP_002827571.1  75 TSRAFRNDQLALFYEEIAALTGSHKVLPMNSGAEAVETAIKAVRKWGYEVKGVAADQAEIIVCANNFHG 143
                                               ********************************************************************* PP

                                 TIGR01885 141 rtlavislstdpesrenfGpyvpnvkkieynnlealeealeeagekvaaflvePiqGeaGvvvpddgyl 209
                                               rt++++  stdp+s+++fGp++p+++ +++++++a++ a++e   + +aflvePiqGeaGv+vp  gy+
  lcl|NCBI__GCF_000018545.1:YP_002827571.1 144 RTIGIVGFSTDPDSHDGFGPFAPGFRIVPFGDIDAFRAAISE---NTVAFLVEPIQGEAGVIVPPAGYF 209
                                               ***************************************998...899********************* PP

                                 TIGR01885 210 kkvrelckkynvlliadeiqtGiartGkllaveheevkPdivllGkalsgGvyPvsavladkevmltik 278
                                                +vrelc+k+ + l+ deiqtG++rtGklla ehe +  d+ l+GkalsgG+yPvsavl+++ev+ ++k
  lcl|NCBI__GCF_000018545.1:YP_002827571.1 210 AEVRELCTKHAITLVLDEIQTGLGRTGKLLAEEHEAIEADVTLIGKALSGGFYPVSAVLSNSEVLGVLK 278
                                               ********************************************************************* PP

                                 TIGR01885 279 pgehGstygGnPlasavavaalevlkeeklaeraeklGeelreelkklkkeivkevrGkGllnaivide 347
                                               pg+hGst+gGnPla+a+a aal+vl+ee ++e+++++Ge++ + l++++++i++evrG+Gl+ a+ + +
  lcl|NCBI__GCF_000018545.1:YP_002827571.1 279 PGQHGSTFGGNPLACAIARAALKVLTEEGMIENSARMGERFMTGLTDIRSNIIREVRGRGLMLAVELVP 347
                                               ********************************************************************9 PP

                                 TIGR01885 348 skangreawdlclklkekGllakptheeiirlaPPlviteeelkeaveiikkv 400
                                               ++     a + c  lk +G+lak+th++ ir+aPPlvit  e+++a+e ++ v
  lcl|NCBI__GCF_000018545.1:YP_002827571.1 348 EA---GGARKYCEALKARGILAKDTHGDTIRIAPPLVITAGEVDWALEQFAAV 397
                                               99...677889***********************************9988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (402 nodes)
Target sequences:                          1  (401 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: 8.98
//
[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