Alignments for a candidate for OAT in Paucidesulfovibrio gracilis DSM 16080

GapMind for Amino acid biosynthesis

Alignments for a candidate for OAT in Paucidesulfovibrio gracilis DSM 16080

Align Ornithine aminotransferase; OAT; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 (characterized)
to candidate WP_078718069.1 B5D49_RS12615 ornithine--oxo-acid transaminase

Query= SwissProt::P38021
         (401 letters)



>NCBI__GCF_900167125.1:WP_078718069.1
          Length = 399

 Score =  466 bits (1200), Expect = e-136
 Identities = 221/396 (55%), Positives = 289/396 (72%), Gaps = 3/396 (0%)

Query: 6   KSKEIIDQTSHYGANNYHPLPIVISEALGAWVKDPEGNEYMDMLSAYSAVNQGHRHPKII 65
           K ++ ID  + YGA NY PL +V+S+  G WV D E N YMD LSAYSAVNQGH HP+I+
Sbjct: 2   KPQDYIDLENRYGAQNYKPLDVVLSKGEGVWVWDVEDNRYMDCLSAYSAVNQGHCHPRIV 61

Query: 66  QALKDQADKITLTSRAFHNDQLGPFYEKTAKLTGKEMILPMNTGAEAVESAVKAARRWAY 125
            AL++QA+++ LTSRAF NDQLG  YE+  +LT    +LPMN+GAEAVE+A+KA R+W Y
Sbjct: 62  AALQEQAERLPLTSRAFRNDQLGLLYEELCRLTNSHKVLPMNSGAEAVETAIKAVRKWGY 121

Query: 126 EVKGVADNQAEIIACVGNFHGRTMLAVSLSSEEEYKRGFGPMLPGIKLIPYGDVEALRQA 185
             KGV +NQAEII C  NFHGRT+  VS S++   + GFGP  PG ++IP+GD +A  QA
Sbjct: 122 MEKGVPENQAEIIVCANNFHGRTISIVSFSTDSGARAGFGPFTPGFRVIPFGDAQAFEQA 181

Query: 186 ITPNTAAFLFEPIQGEAGIVIPPEGFLQEAAAICKEENVLFIADEIQTGLGRTGKTFACD 245
           ITP+T A L EPIQGEAG++IPPEG+L+    +C    +  I DEIQTGLGRTGK  A +
Sbjct: 182 ITPHTVALLVEPIQGEAGVIIPPEGYLRRVRELCDTHGIQLILDEIQTGLGRTGKLLAEE 241

Query: 246 WDGIVPDMYILGKALGGGVFPISCIAADREILGVFNPGSHGSTFGGNPLACAVSIASLEV 305
            +GI  D+ ++GKAL GG++P+S + ++ E+LG+  PG HGSTFGGNPLACAV+ A+L V
Sbjct: 242 HEGIEADITLIGKALSGGLYPVSAVLSNTEVLGILRPGEHGSTFGGNPLACAVARAALNV 301

Query: 306 LEDEKLADRSLELGEYFKSELESIDSPVIKEVRGRGLFIGVELTEA---ARPYCERLKEE 362
           L +E L   +  +G+ F   L +I +P +++VRGRGL + VEL  +   ARPYCERLKE 
Sbjct: 302 LVEEGLIANAELMGQRFMKGLRAIANPAVRDVRGRGLLLAVELDPSAGGARPYCERLKEA 361

Query: 363 GLLCKETHDTVIRFAPPLIISKEDLDWAIEKIKHVL 398
           GLLCKETH+  IRFAPPL+I+ E +DWA+E+I  VL
Sbjct: 362 GLLCKETHENTIRFAPPLVITAEQVDWALERISSVL 397


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: 466
Number of extensions: 11
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: 399
Length adjustment: 31
Effective length of query: 370
Effective length of database: 368
Effective search space:   136160
Effective search space used:   136160
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_078718069.1 B5D49_RS12615 (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.2177159.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.9e-169  548.5   0.0   4.4e-169  548.4   0.0    1.0  1  NCBI__GCF_900167125.1:WP_078718069.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900167125.1:WP_078718069.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  548.4   0.0  4.4e-169  4.4e-169       2     401 ..       4     397 ..       3     398 .. 0.98

  Alignments for each domain:
  == domain 1  score: 548.4 bits;  conditional E-value: 4.4e-169
                             TIGR01885   2 eevieleekygahnyhplpvvlskaeGakvwdvegkryldflsaysavnqGhchpkivkalveqaqkltlssr 74 
                                           +++i+le++yga+ny+pl+vvlsk+eG+ vwdve++ry+d lsaysavnqGhchp+iv+al eqa++l l+sr
  NCBI__GCF_900167125.1:WP_078718069.1   4 QDYIDLENRYGAQNYKPLDVVLSKGEGVWVWDVEDNRYMDCLSAYSAVNQGHCHPRIVAALQEQAERLPLTSR 76 
                                           6899********************************************************************* PP

                             TIGR01885  75 afyndvfgefaeyvtklfGydkvlpmntGaeavetaiklarkWgykkkkipedkalilsaegnfhGrtlavis 147
                                           af nd++g + e +++l    kvlpmn+Gaeavetaik +rkWgy++k++pe++a i+++++nfhGrt++++s
  NCBI__GCF_900167125.1:WP_078718069.1  77 AFRNDQLGLLYEELCRLTNSHKVLPMNSGAEAVETAIKAVRKWGYMEKGVPENQAEIIVCANNFHGRTISIVS 149
                                           ************************************************************************* PP

                             TIGR01885 148 lstdpesrenfGpyvpnvkkieynnlealeealeeagekvaaflvePiqGeaGvvvpddgylkkvrelckkyn 220
                                            std  +r +fGp++p+++ i++++++a+e+a++    + +a+lvePiqGeaGv++p +gyl++vrelc+ + 
  NCBI__GCF_900167125.1:WP_078718069.1 150 FSTDSGARAGFGPFTPGFRVIPFGDAQAFEQAITP---HTVALLVEPIQGEAGVIIPPEGYLRRVRELCDTHG 219
                                           *******************************9987...7889******************************* PP

                             TIGR01885 221 vlliadeiqtGiartGkllaveheevkPdivllGkalsgGvyPvsavladkevmltikpgehGstygGnPlas 293
                                           + li deiqtG++rtGklla ehe++  di l+GkalsgG+yPvsavl++ ev+ +++pgehGst+gGnPla+
  NCBI__GCF_900167125.1:WP_078718069.1 220 IQLILDEIQTGLGRTGKLLAEEHEGIEADITLIGKALSGGLYPVSAVLSNTEVLGILRPGEHGSTFGGNPLAC 292
                                           ************************************************************************* PP

                             TIGR01885 294 avavaalevlkeeklaeraeklGeelreelkklkkeivkevrGkGllnaivideskangreawdlclklkekG 366
                                           ava aal+vl ee l+ +ae +G+++ + l+++ ++ v++vrG+Gll a+ +d+s+     a   c +lke G
  NCBI__GCF_900167125.1:WP_078718069.1 293 AVARAALNVLVEEGLIANAELMGQRFMKGLRAIANPAVRDVRGRGLLLAVELDPSA---GGARPYCERLKEAG 362
                                           *******************************************************9...567789******** PP

                             TIGR01885 367 llakptheeiirlaPPlviteeelkeaveiikkvl 401
                                           ll k+the+ ir+aPPlvit e++++a+e i++vl
  NCBI__GCF_900167125.1:WP_078718069.1 363 LLCKETHENTIRFAPPLVITAEQVDWALERISSVL 397
                                           *****************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (402 nodes)
Target sequences:                          1  (399 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 30.15
//
[ok]

This GapMind analysis is from Jul 25 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 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