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.23006.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.53
//
[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:

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:

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:

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:

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