Alignments for a candidate for OAT in Dechloromonas agitata is5

GapMind for Amino acid biosynthesis

Alignments for a candidate for OAT in Dechloromonas agitata is5

Align Ornithine aminotransferase; OAT; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 (characterized)
to candidate WP_084019650.1 K420_RS19775 ornithine--oxo-acid transaminase

Query= SwissProt::P38021
         (401 letters)



>NCBI__GCF_000519045.1:WP_084019650.1
          Length = 697

 Score =  440 bits (1132), Expect = e-128
 Identities = 214/389 (55%), Positives = 281/389 (72%), Gaps = 5/389 (1%)

Query: 17  YGANNYHPLPIVISEALGAWVKDPEGNEYMDMLSAYSAVNQGHRHPKIIQALKDQADKIT 76
           +GA NY PLP+V+S   G WV D EG  Y+DM+SAYSA + GH HP+++ AL  QA ++ 
Sbjct: 300 FGARNYAPLPVVLSAGSGCWVSDTEGRRYLDMMSAYSANSFGHAHPRLLAALNAQAGRLA 359

Query: 77  LTSRAFHNDQLGPFYEKTAKLTGKEMILPMNTGAEAVESAVKAARRWAYEVKGVADNQAE 136
           LTSRA+ ND+L     + A L+G E +LP+NTG EAVE+A+KAAR+WAY+VKGV   +AE
Sbjct: 360 LTSRAYSNDRLPLLLRRLALLSGYERVLPVNTGLEAVETALKAARKWAYQVKGVPPGKAE 419

Query: 137 IIACVGNFHGRTMLAVSLSSEEEYKRGFGPMLPGIKLIPYGDVEALRQAITPNTAAFLFE 196
           IIAC GNFHGR++  V LSSE +Y+ GFGP  PG+K +P+ DV AL  AITP+TAAFL E
Sbjct: 420 IIACQGNFHGRSIAIVGLSSEAQYRDGFGPFPPGLKTVPFADVAALAAAITPHTAAFLVE 479

Query: 197 PIQGEAGIVIPPEGFLQEAAAICKEENVLFIADEIQTGLGRTGKTFACDWDGIVPDMYIL 256
           PIQGE G+++PP G+L   AA+C+   VL I DE+QTGLGRTGK FA   + + PD  IL
Sbjct: 480 PIQGEGGVIMPPPGYLSACAALCRRHGVLLIVDEVQTGLGRTGKLFAYQHEPLRPDGIIL 539

Query: 257 GKALGGGVFPISCIAADREILGVFNPGSHGSTFGGNPLACAVSIASLEVLEDEKLADRSL 316
           GKALGGG+ P+S   AD  ++ VF PG HGSTFGGNPLA AV++++L++LEDE L + + 
Sbjct: 540 GKALGGGLLPVSAFLADDALMRVFTPGDHGSTFGGNPLAAAVALSALDLLEDEGLVEHAA 599

Query: 317 ELGEYFKSELESI--DSPVIKEVRGRGLFIGVELTEA---ARPYCERLKEEGLLCKETHD 371
            LGE+  + L  +   +PV++ VRG+GLF G+EL      AR   ERL + G+L K+TH 
Sbjct: 600 RLGEHLLARLNELAATTPVVRAVRGKGLFAGIELEPTLADARDMAERLLQHGILTKDTHT 659

Query: 372 TVIRFAPPLIISKEDLDWAIEKIKHVLRN 400
           TV+R APPLII +  LDWA+++I  VLRN
Sbjct: 660 TVLRLAPPLIIDRPTLDWALDEITVVLRN 688


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: 758
Number of extensions: 26
Number of successful extensions: 3
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: 697
Length adjustment: 35
Effective length of query: 366
Effective length of database: 662
Effective search space:   242292
Effective search space used:   242292
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: 52 (24.6 bits)

Align candidate WP_084019650.1 K420_RS19775 (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.15776.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.3e-148  480.9   0.0   1.7e-148  480.5   0.0    1.1  1  lcl|NCBI__GCF_000519045.1:WP_084019650.1  K420_RS19775 ornithine--oxo-acid


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000519045.1:WP_084019650.1  K420_RS19775 ornithine--oxo-acid transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  480.5   0.0  1.7e-148  1.7e-148       4     400 ..     293     685 ..     290     687 .. 0.98

  Alignments for each domain:
  == domain 1  score: 480.5 bits;  conditional E-value: 1.7e-148
                                 TIGR01885   4 vieleekygahnyhplpvvlskaeGakvwdvegkryldflsaysavnqGhchpkivkalveqaqkltls 72 
                                               + ++e+ +ga+ny plpvvls ++G  v d+eg+ryld++saysa + Gh+hp++++al  qa +l+l+
  lcl|NCBI__GCF_000519045.1:WP_084019650.1 293 LQRWENGFGARNYAPLPVVLSAGSGCWVSDTEGRRYLDMMSAYSANSFGHAHPRLLAALNAQAGRLALT 361
                                               56799**************************************************************** PP

                                 TIGR01885  73 srafyndvfgefaeyvtklfGydkvlpmntGaeavetaiklarkWgykkkkipedkalilsaegnfhGr 141
                                               sra+ nd ++ + + ++ l Gy++vlp+ntG eaveta+k arkW+y++k++p  ka i++++gnfhGr
  lcl|NCBI__GCF_000519045.1:WP_084019650.1 362 SRAYSNDRLPLLLRRLALLSGYERVLPVNTGLEAVETALKAARKWAYQVKGVPPGKAEIIACQGNFHGR 430
                                               ********************************************************************* PP

                                 TIGR01885 142 tlavislstdpesrenfGpyvpnvkkieynnlealeealeeagekvaaflvePiqGeaGvvvpddgylk 210
                                               ++a++ ls++ + r++fGp+ p++k++++ +++al  a++    + aaflvePiqGe Gv++p  gyl 
  lcl|NCBI__GCF_000519045.1:WP_084019650.1 431 SIAIVGLSSEAQYRDGFGPFPPGLKTVPFADVAALAAAITP---HTAAFLVEPIQGEGGVIMPPPGYLS 496
                                               ************************************99987...89*********************** PP

                                 TIGR01885 211 kvrelckkynvlliadeiqtGiartGkllaveheevkPdivllGkalsgGvyPvsavladkevmltikp 279
                                                + +lc+++ vlli+de+qtG++rtGkl+a++he ++Pd ++lGkal+gG++Pvsa lad+++m +++p
  lcl|NCBI__GCF_000519045.1:WP_084019650.1 497 ACAALCRRHGVLLIVDEVQTGLGRTGKLFAYQHEPLRPDGIILGKALGGGLLPVSAFLADDALMRVFTP 565
                                               ********************************************************************* PP

                                 TIGR01885 280 gehGstygGnPlasavavaalevlkeeklaeraeklGeelreelkkl..kkeivkevrGkGllnaivid 346
                                               g+hGst+gGnPla+ava+ al++l++e l+e+a++lGe+l ++l++l  ++++v+ vrGkGl+++i ++
  lcl|NCBI__GCF_000519045.1:WP_084019650.1 566 GDHGSTFGGNPLAAAVALSALDLLEDEGLVEHAARLGEHLLARLNELaaTTPVVRAVRGKGLFAGIELE 634
                                               **********************************************976679***************** PP

                                 TIGR01885 347 eskangreawdlclklkekGllakptheeiirlaPPlviteeelkeaveiikkv 400
                                               ++    ++a d+  +l ++G+l+k+th++++rlaPPl+i +  l++a++ i+ v
  lcl|NCBI__GCF_000519045.1:WP_084019650.1 635 PTL---ADARDMAERLLQHGILTKDTHTTVLRLAPPLIIDRPTLDWALDEITVV 685
                                               **9...78999************************************9988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (402 nodes)
Target sequences:                          1  (697 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: 18.83
//
[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