GapMind for catabolism of small carbon sources

 

Aligments for a candidate for astC in Marinobacter adhaerens HP15

Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate GFF3099 HP15_3042 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein

Query= reanno::Marino:GFF3099
         (404 letters)



>lcl|FitnessBrowser__Marino:GFF3099 HP15_3042 bifunctional
           N-succinyldiaminopimelate-
           aminotransferase/acetylornithine transaminase protein
          Length = 404

 Score =  810 bits (2091), Expect = 0.0
 Identities = 404/404 (100%), Positives = 404/404 (100%)

Query: 1   MNKEPVSRELFDEVMVPNYAPGSIIPVRGEGSRIWDQEGREFIDLQGGIAVTCLGHSHPG 60
           MNKEPVSRELFDEVMVPNYAPGSIIPVRGEGSRIWDQEGREFIDLQGGIAVTCLGHSHPG
Sbjct: 1   MNKEPVSRELFDEVMVPNYAPGSIIPVRGEGSRIWDQEGREFIDLQGGIAVTCLGHSHPG 60

Query: 61  LVGALHDQAEKIWHLSNVMTNEPALRLAKTLCDLTFAERVFFANSGAEANEAAFKLARRY 120
           LVGALHDQAEKIWHLSNVMTNEPALRLAKTLCDLTFAERVFFANSGAEANEAAFKLARRY
Sbjct: 61  LVGALHDQAEKIWHLSNVMTNEPALRLAKTLCDLTFAERVFFANSGAEANEAAFKLARRY 120

Query: 121 AWEHHGKEKNEIISFKNSFHGRTLFTVSVGGQPKYLEGFEPAPGGIHHAEFNDLESVKKL 180
           AWEHHGKEKNEIISFKNSFHGRTLFTVSVGGQPKYLEGFEPAPGGIHHAEFNDLESVKKL
Sbjct: 121 AWEHHGKEKNEIISFKNSFHGRTLFTVSVGGQPKYLEGFEPAPGGIHHAEFNDLESVKKL 180

Query: 181 ISKEKTCAIVVEPIQGEGGVMPGDQAFLQGLRDLCDENDALLVFDEVQSGVGRSGHFYAY 240
           ISKEKTCAIVVEPIQGEGGVMPGDQAFLQGLRDLCDENDALLVFDEVQSGVGRSGHFYAY
Sbjct: 181 ISKEKTCAIVVEPIQGEGGVMPGDQAFLQGLRDLCDENDALLVFDEVQSGVGRSGHFYAY 240

Query: 241 QMYGVVPDILSSAKGLGGGFPVAAMLTTAKVAASLGVGTHGSTYGGNALACAVAQRVVDT 300
           QMYGVVPDILSSAKGLGGGFPVAAMLTTAKVAASLGVGTHGSTYGGNALACAVAQRVVDT
Sbjct: 241 QMYGVVPDILSSAKGLGGGFPVAAMLTTAKVAASLGVGTHGSTYGGNALACAVAQRVVDT 300

Query: 301 VSQPEILKGVKARSDKLRKGMMDIGERYGVFTEVRGAGLLLGCVLTEKWQGKAKDFLNAG 360
           VSQPEILKGVKARSDKLRKGMMDIGERYGVFTEVRGAGLLLGCVLTEKWQGKAKDFLNAG
Sbjct: 301 VSQPEILKGVKARSDKLRKGMMDIGERYGVFTEVRGAGLLLGCVLTEKWQGKAKDFLNAG 360

Query: 361 LEEGVMVLVAGANVIRLAPSLIIPEPDIELALERFEAAVKKLTA 404
           LEEGVMVLVAGANVIRLAPSLIIPEPDIELALERFEAAVKKLTA
Sbjct: 361 LEEGVMVLVAGANVIRLAPSLIIPEPDIELALERFEAAVKKLTA 404


Lambda     K      H
   0.318    0.137    0.406 

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: 782
Number of extensions: 19
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: 404
Length of database: 404
Length adjustment: 31
Effective length of query: 373
Effective length of database: 373
Effective search space:   139129
Effective search space used:   139129
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate GFF3099 HP15_3042 (bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein)
to HMM TIGR03246 (astC: succinylornithine transaminase family (EC 2.6.1.81))

# 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/TIGR03246.hmm
# target sequence database:        /tmp/gapView.18660.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03246  [M=397]
Accession:   TIGR03246
Description: arg_catab_astC: succinylornithine transaminase family
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.2e-205  668.9   0.1   1.4e-205  668.7   0.1    1.0  1  lcl|FitnessBrowser__Marino:GFF3099  HP15_3042 bifunctional N-succiny


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF3099  HP15_3042 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  668.7   0.1  1.4e-205  1.4e-205       1     396 [.       6     402 ..       6     403 .. 0.99

  Alignments for each domain:
  == domain 1  score: 668.7 bits;  conditional E-value: 1.4e-205
                           TIGR03246   1 veresfdevmvpvyapakfipvrgeGsrvwdqegkeyidfaGGiavnalGhahpelvealkeqaeklwhlgngyt 75 
                                         v+re fdevmvp+yap+++ipvrgeGsr+wdqeg+e+id+ GGiav++lGh+hp lv al++qaek+whl+n++t
  lcl|FitnessBrowser__Marino:GFF3099   6 VSRELFDEVMVPNYAPGSIIPVRGEGSRIWDQEGREFIDLQGGIAVTCLGHSHPGLVGALHDQAEKIWHLSNVMT 80 
                                         78************************************************************************* PP

                           TIGR03246  76 nepvlrlakklvdatfadkvffcnsGaeaneaalklarkvaldkygaekseivafknsfhGrtlftvsvGGqaky 150
                                         nep+lrlak l d tfa++vff+nsGaeaneaa+klar++a++++g+ek+ei++fknsfhGrtlftvsvGGq+ky
  lcl|FitnessBrowser__Marino:GFF3099  81 NEPALRLAKTLCDLTFAERVFFANSGAEANEAAFKLARRYAWEHHGKEKNEIISFKNSFHGRTLFTVSVGGQPKY 155
                                         *************************************************************************** PP

                           TIGR03246 151 sedfaplpegikhaayndlealkalis.dktcavivepiqGegGvvpadkaflkglrelcdrhnallifdevqtG 224
                                          e+f+p p+gi+ha++ndle++k+lis +ktca++vepiqGegGv+p d+afl+glr+lcd+ +all+fdevq+G
  lcl|FitnessBrowser__Marino:GFF3099 156 LEGFEPAPGGIHHAEFNDLESVKKLISkEKTCAIVVEPIQGEGGVMPGDQAFLQGLRDLCDENDALLVFDEVQSG 230
                                         **************************7479********************************************* PP

                           TIGR03246 225 vGrtGelyaymeyGvtpdiltsakalGgGfpiGalltteelakvlkvGthGttyGGnplacavaekvldlvntae 299
                                         vGr G++yay+ yGv+pdil+sak+lGgGfp+ a+ltt ++a++l vGthG+tyGGn lacava++v+d+v+++e
  lcl|FitnessBrowser__Marino:GFF3099 231 VGRSGHFYAYQMYGVVPDILSSAKGLGGGFPVAAMLTTAKVAASLGVGTHGSTYGGNALACAVAQRVVDTVSQPE 305
                                         *************************************************************************** PP

                           TIGR03246 300 lleGvkqrhelfvdelekinarykvfseirGkGlliGavlteeyaGkakdlvnaaaeeGvlvliaGpdvvrfaps 374
                                         +l+Gvk+r++++ + +  i++ry vf+e+rG Gll+G+vlte+++Gkakd++na  eeGv+vl+aG++v+r+aps
  lcl|FitnessBrowser__Marino:GFF3099 306 ILKGVKARSDKLRKGMMDIGERYGVFTEVRGAGLLLGCVLTEKWQGKAKDFLNAGLEEGVMVLVAGANVIRLAPS 380
                                         *************************************************************************** PP

                           TIGR03246 375 lvieeeeikeGlarlekavekl 396
                                         l+i+e +i+  l+r+e av+kl
  lcl|FitnessBrowser__Marino:GFF3099 381 LIIPEPDIELALERFEAAVKKL 402
                                         *******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (397 nodes)
Target sequences:                          1  (404 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.51
//
[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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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