Alignments for a candidate for OAT in Pontibacter ramchanderi LP43

GapMind for Amino acid biosynthesis

Alignments for a candidate for OAT in Pontibacter ramchanderi LP43

Align Ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate WP_101444294.1 BD749_RS10520 ornithine--oxo-acid transaminase

Query= reanno::Cola:Echvi_0577
         (413 letters)



>NCBI__GCF_002846395.1:WP_101444294.1
          Length = 413

 Score =  566 bits (1459), Expect = e-166
 Identities = 274/408 (67%), Positives = 333/408 (81%), Gaps = 1/408 (0%)

Query: 5   ITSSQQAIELENKHGAHNYHPLPVVLSRGEGVFMWDVEGEKYYDFLSSYSAVNQGHCHPR 64
           ITSSQQAIE E K+GAHNYHPLPVVLS+GEGV++WDVEG++YYDFLS+YSAVNQGHCHPR
Sbjct: 6   ITSSQQAIETEEKYGAHNYHPLPVVLSKGEGVYLWDVEGKRYYDFLSAYSAVNQGHCHPR 65

Query: 65  ILQTLIDQAGTLTLTSRAFHNDVLGPFEKFLTEYFGYDKVLPMNTGAEGVETAIKIARKW 124
           I+  LI+QA  LTLTSRAF+ND LG  EK++ E FGYDK L MN+GAE VETAIK+ARKW
Sbjct: 66  IINALIEQAQQLTLTSRAFYNDKLGIAEKYICELFGYDKSLYMNSGAEAVETAIKLARKW 125

Query: 125 GYEKKGIPENEGTIIVAKNNFHGRTTTVISFSNDETARKNFGPYTPGFVTIPHDDIDALK 184
           GY KKGI  +   IIV + NFHGRTT +ISFS D  + K FGPY PGF  IP++D++AL+
Sbjct: 126 GYLKKGIAPHNAEIIVVERNFHGRTTGIISFSTDPDSTKGFGPYMPGFKVIPYNDLEALE 185

Query: 185 DVLSQSKNIIGYLVEPIQGEAGVYVPKEGYLKEVAAVCKDHGVLFMADEIQTGIARTGKL 244
             L ++ N+ G+LVEPIQGEAGV VP++GYL +  A+CK++ VL MADEIQTGIARTGK+
Sbjct: 186 TALKENPNVCGFLVEPIQGEAGVVVPQDGYLAKAHALCKEYNVLLMADEIQTGIARTGKM 245

Query: 245 LACDHEGVKPDMLILGKAISGGFYPVSAVLADDHIMEVIQPGQHGSTFGGNPLGAKVAMT 304
           LA  ++ VK D+LILGKA+SGG  PVS VLA+D IM  IQPG+HGSTFGGNP+ A VA+ 
Sbjct: 246 LASYYDDVKADILILGKALSGGVLPVSCVLANDDIMLCIQPGEHGSTFGGNPMAAAVAIA 305

Query: 305 ALNVVKDEKLAENADKLGKLFRERIQQL-VDKSDLVELVRGKGLLNAIVINDTEDSDTAW 363
           AL V+K+E L ENA KLG++FR+R+ QL   + ++V LVRG+GLLNAIVI    D  TAW
Sbjct: 306 ALEVIKEENLVENAYKLGEIFRDRMNQLKAKRPEVVTLVRGRGLLNAIVIEPAADGRTAW 365

Query: 364 RLCLALKENGLLAKPTHGNIIRFAPPLVITEEQLHDCCDIIEKTIQNF 411
            +C+ LKENGLLAKPTHG+IIRFAPPLV+TEEQLH+CCDIIE+ + NF
Sbjct: 366 DVCVELKENGLLAKPTHGDIIRFAPPLVMTEEQLHECCDIIERVVMNF 413


Lambda     K      H
   0.318    0.137    0.407 

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: 589
Number of extensions: 30
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: 413
Length of database: 413
Length adjustment: 31
Effective length of query: 382
Effective length of database: 382
Effective search space:   145924
Effective search space used:   145924
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_101444294.1 BD749_RS10520 (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.833349.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.7e-209  679.3   0.0     9e-209  679.1   0.0    1.0  1  NCBI__GCF_002846395.1:WP_101444294.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002846395.1:WP_101444294.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  679.1   0.0    9e-209    9e-209       1     401 [.       9     410 ..       9     411 .. 0.99

  Alignments for each domain:
  == domain 1  score: 679.1 bits;  conditional E-value: 9e-209
                             TIGR01885   1 seevieleekygahnyhplpvvlskaeGakvwdvegkryldflsaysavnqGhchpkivkalveqaqkltlss 73 
                                           s+++ie+eekygahnyhplpvvlsk+eG+++wdvegkry+dflsaysavnqGhchp+i++al+eqaq+ltl+s
  NCBI__GCF_002846395.1:WP_101444294.1   9 SQQAIETEEKYGAHNYHPLPVVLSKGEGVYLWDVEGKRYYDFLSAYSAVNQGHCHPRIINALIEQAQQLTLTS 81 
                                           689********************************************************************** PP

                             TIGR01885  74 rafyndvfgefaeyvtklfGydkvlpmntGaeavetaiklarkWgykkkkipedkalilsaegnfhGrtlavi 146
                                           rafynd++g  ++y+++lfGydk l mn+GaeavetaiklarkWgy kk+i+ ++a i+++e+nfhGrt ++i
  NCBI__GCF_002846395.1:WP_101444294.1  82 RAFYNDKLGIAEKYICELFGYDKSLYMNSGAEAVETAIKLARKWGYLKKGIAPHNAEIIVVERNFHGRTTGII 154
                                           ************************************************************************* PP

                             TIGR01885 147 slstdpesrenfGpyvpnvkkieynnlealeealeeagekvaaflvePiqGeaGvvvpddgylkkvrelckky 219
                                           s stdp+s+++fGpy+p++k i+yn+leale al+e +++v++flvePiqGeaGvvvp+dgyl k+++lck+y
  NCBI__GCF_002846395.1:WP_101444294.1 155 SFSTDPDSTKGFGPYMPGFKVIPYNDLEALETALKE-NPNVCGFLVEPIQGEAGVVVPQDGYLAKAHALCKEY 226
                                           ***********************************9.9*********************************** PP

                             TIGR01885 220 nvlliadeiqtGiartGkllaveheevkPdivllGkalsgGvyPvsavladkevmltikpgehGstygGnPla 292
                                           nvll+adeiqtGiartGk+la+ +++vk di++lGkalsgGv+Pvs+vla++++ml+i+pgehGst+gGnP+a
  NCBI__GCF_002846395.1:WP_101444294.1 227 NVLLMADEIQTGIARTGKMLASYYDDVKADILILGKALSGGVLPVSCVLANDDIMLCIQPGEHGSTFGGNPMA 299
                                           ************************************************************************* PP

                             TIGR01885 293 savavaalevlkeeklaeraeklGeelreelkklkk...eivkevrGkGllnaivideskangreawdlclkl 362
                                           +ava+aalev+kee+l+e+a klGe++r+++++lk    e+v+ vrG+Gllnaivi++ + +gr+awd+c+ l
  NCBI__GCF_002846395.1:WP_101444294.1 300 AAVAIAALEVIKEENLVENAYKLGEIFRDRMNQLKAkrpEVVTLVRGRGLLNAIVIEPAA-DGRTAWDVCVEL 371
                                           ******************************9999443449*****************998.************ PP

                             TIGR01885 363 kekGllakptheeiirlaPPlviteeelkeaveiikkvl 401
                                           ke+Gllakpth++iir+aPPlv+tee+l+e+++ii++v+
  NCBI__GCF_002846395.1:WP_101444294.1 372 KENGLLAKPTHGDIIRFAPPLVMTEEQLHECCDIIERVV 410
                                           ***********************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (402 nodes)
Target sequences:                          1  (413 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: 25.62
//
[ok]

This GapMind analysis is from Jul 26 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 2024 update 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 original 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