GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Marino:GFF3099
          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.8776.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: 9.41
//
[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