Alignments for a candidate for rocD in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for rocD in Echinicola vietnamensis KMM 6221, DSM 17526

Align Ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate Echvi_0577 Echvi_0577 ornithine aminotransferase

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



>FitnessBrowser__Cola:Echvi_0577
          Length = 413

 Score =  838 bits (2164), Expect = 0.0
 Identities = 413/413 (100%), Positives = 413/413 (100%)

Query: 1   MMQPITSSQQAIELENKHGAHNYHPLPVVLSRGEGVFMWDVEGEKYYDFLSSYSAVNQGH 60
           MMQPITSSQQAIELENKHGAHNYHPLPVVLSRGEGVFMWDVEGEKYYDFLSSYSAVNQGH
Sbjct: 1   MMQPITSSQQAIELENKHGAHNYHPLPVVLSRGEGVFMWDVEGEKYYDFLSSYSAVNQGH 60

Query: 61  CHPRILQTLIDQAGTLTLTSRAFHNDVLGPFEKFLTEYFGYDKVLPMNTGAEGVETAIKI 120
           CHPRILQTLIDQAGTLTLTSRAFHNDVLGPFEKFLTEYFGYDKVLPMNTGAEGVETAIKI
Sbjct: 61  CHPRILQTLIDQAGTLTLTSRAFHNDVLGPFEKFLTEYFGYDKVLPMNTGAEGVETAIKI 120

Query: 121 ARKWGYEKKGIPENEGTIIVAKNNFHGRTTTVISFSNDETARKNFGPYTPGFVTIPHDDI 180
           ARKWGYEKKGIPENEGTIIVAKNNFHGRTTTVISFSNDETARKNFGPYTPGFVTIPHDDI
Sbjct: 121 ARKWGYEKKGIPENEGTIIVAKNNFHGRTTTVISFSNDETARKNFGPYTPGFVTIPHDDI 180

Query: 181 DALKDVLSQSKNIIGYLVEPIQGEAGVYVPKEGYLKEVAAVCKDHGVLFMADEIQTGIAR 240
           DALKDVLSQSKNIIGYLVEPIQGEAGVYVPKEGYLKEVAAVCKDHGVLFMADEIQTGIAR
Sbjct: 181 DALKDVLSQSKNIIGYLVEPIQGEAGVYVPKEGYLKEVAAVCKDHGVLFMADEIQTGIAR 240

Query: 241 TGKLLACDHEGVKPDMLILGKAISGGFYPVSAVLADDHIMEVIQPGQHGSTFGGNPLGAK 300
           TGKLLACDHEGVKPDMLILGKAISGGFYPVSAVLADDHIMEVIQPGQHGSTFGGNPLGAK
Sbjct: 241 TGKLLACDHEGVKPDMLILGKAISGGFYPVSAVLADDHIMEVIQPGQHGSTFGGNPLGAK 300

Query: 301 VAMTALNVVKDEKLAENADKLGKLFRERIQQLVDKSDLVELVRGKGLLNAIVINDTEDSD 360
           VAMTALNVVKDEKLAENADKLGKLFRERIQQLVDKSDLVELVRGKGLLNAIVINDTEDSD
Sbjct: 301 VAMTALNVVKDEKLAENADKLGKLFRERIQQLVDKSDLVELVRGKGLLNAIVINDTEDSD 360

Query: 361 TAWRLCLALKENGLLAKPTHGNIIRFAPPLVITEEQLHDCCDIIEKTIQNFKK 413
           TAWRLCLALKENGLLAKPTHGNIIRFAPPLVITEEQLHDCCDIIEKTIQNFKK
Sbjct: 361 TAWRLCLALKENGLLAKPTHGNIIRFAPPLVITEEQLHDCCDIIEKTIQNFKK 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: 803
Number of extensions: 29
Number of successful extensions: 1
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 Echvi_0577 Echvi_0577 (ornithine aminotransferase)
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.carbon/TIGR01885.hmm
# target sequence database:        /tmp/gapView.22903.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   1.1e-203  662.3   0.0   1.3e-203  662.1   0.0    1.0  1  lcl|FitnessBrowser__Cola:Echvi_0577  Echvi_0577 ornithine aminotransf


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_0577  Echvi_0577 ornithine aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  662.1   0.0  1.3e-203  1.3e-203       1     402 []       8     409 ..       8     409 .. 0.99

  Alignments for each domain:
  == domain 1  score: 662.1 bits;  conditional E-value: 1.3e-203
                            TIGR01885   1 seevieleekygahnyhplpvvlskaeGakvwdvegkryldflsaysavnqGhchpkivkalveqaqkltlssr 74 
                                          s+++iele+k+gahnyhplpvvls++eG+++wdveg++y+dfls+ysavnqGhchp+i+++l++qa +ltl+sr
  lcl|FitnessBrowser__Cola:Echvi_0577   8 SQQAIELENKHGAHNYHPLPVVLSRGEGVFMWDVEGEKYYDFLSSYSAVNQGHCHPRILQTLIDQAGTLTLTSR 81 
                                          689*********************************************************************** PP

                            TIGR01885  75 afyndvfgefaeyvtklfGydkvlpmntGaeavetaiklarkWgykkkkipedkalilsaegnfhGrtlavisl 148
                                          af+ndv+g f++++t++fGydkvlpmntGae+vetaik+arkWgy+kk+ipe++ +i++a++nfhGrt +vis 
  lcl|FitnessBrowser__Cola:Echvi_0577  82 AFHNDVLGPFEKFLTEYFGYDKVLPMNTGAEGVETAIKIARKWGYEKKGIPENEGTIIVAKNNFHGRTTTVISF 155
                                          ************************************************************************** PP

                            TIGR01885 149 stdpesrenfGpyvpnvkkieynnlealeealeeagekvaaflvePiqGeaGvvvpddgylkkvrelckkynvl 222
                                          s+d+++r+nfGpy+p++ +i++++++al+++l++ ++++ ++lvePiqGeaGv vp++gylk+v ++ck + vl
  lcl|FitnessBrowser__Cola:Echvi_0577 156 SNDETARKNFGPYTPGFVTIPHDDIDALKDVLSQ-SKNIIGYLVEPIQGEAGVYVPKEGYLKEVAAVCKDHGVL 228
                                          *********************************9.99************************************* PP

                            TIGR01885 223 liadeiqtGiartGkllaveheevkPdivllGkalsgGvyPvsavladkevmltikpgehGstygGnPlasava 296
                                          ++adeiqtGiartGklla++he+vkPd+++lGka+sgG+yPvsavlad+++m +i+pg+hGst+gGnPl+++va
  lcl|FitnessBrowser__Cola:Echvi_0577 229 FMADEIQTGIARTGKLLACDHEGVKPDMLILGKAISGGFYPVSAVLADDHIMEVIQPGQHGSTFGGNPLGAKVA 302
                                          ************************************************************************** PP

                            TIGR01885 297 vaalevlkeeklaeraeklGeelreelkkl..kkeivkevrGkGllnaivideskangreawdlclklkekGll 368
                                          + al+v+k+eklae+a+klG+ +re++++l  k+++v+ vrGkGllnaivi++++ ++ +aw lcl lke+Gll
  lcl|FitnessBrowser__Cola:Echvi_0577 303 MTALNVVKDEKLAENADKLGKLFRERIQQLvdKSDLVELVRGKGLLNAIVINDTE-DSDTAWRLCLALKENGLL 375
                                          *****************************987789******************99.9***************** PP

                            TIGR01885 369 akptheeiirlaPPlviteeelkeaveiikkvlk 402
                                          akpth++iir+aPPlvitee+l+++++ii+k+++
  lcl|FitnessBrowser__Cola:Echvi_0577 376 AKPTHGNIIRFAPPLVITEEQLHDCCDIIEKTIQ 409
                                          *******************************985 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.19
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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

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 catabolism of small carbon sources