GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Halomonas xinjiangensis TRM 0175

Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_043529620.1 JH15_RS09230 aspartate aminotransferase family protein

Query= BRENDA::O30508
         (406 letters)



>NCBI__GCF_000759345.1:WP_043529620.1
          Length = 404

 Score =  527 bits (1357), Expect = e-154
 Identities = 248/395 (62%), Positives = 322/395 (81%)

Query: 10  RADFDRYMVPNYAPAAFIPVRGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTE 69
           R+DFD+YM PNY+P   IPVRG+GSR+WDQ GRE IDFAGGIAV +LGH HP LV+AL  
Sbjct: 7   RSDFDQYMAPNYSPQQVIPVRGKGSRLWDQEGREYIDFAGGIAVNALGHCHPVLVEALKT 66

Query: 70  QAQRIWHVSNVFTNEPALRLARKLVDATFAERVFLANSGAEANEAAFKLARRYANDVYGP 129
           Q + +WH+SNV+TNEPAL+LA+ LV+ TFA++VFL +SG EANEAA KLARRY  + +G 
Sbjct: 67  QGETLWHLSNVYTNEPALKLAKSLVERTFADKVFLCSSGGEANEAALKLARRYIYEKHGE 126

Query: 130 QKYEIIAASNSFHGRTLFTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALKAAISDKTCA 189
           QK +II+   SFHGRT FTV+VGGQPKYS GFGP   GI H  YNDL++++A I D TCA
Sbjct: 127 QKDKIISFRQSFHGRTFFTVSVGGQPKYSQGFGPVPGGIQHAEYNDLDSVRALIDDNTCA 186

Query: 190 VVLEPIQGEGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGVVPD 249
           +++EP+QGEGG++PA Q +L G R+LCD+H ALL+FDEVQ+G+GR G+ FAYMHYGV PD
Sbjct: 187 IMVEPMQGEGGIVPATQEFLSGLRELCDQHQALLIFDEVQTGVGRSGKFFAYMHYGVTPD 246

Query: 250 ILSSAKSLGGGFPIGAMLTTGEIAKHLSVGTHGTTYGGNPLASAVAEAALDVINTPEVLD 309
           IL+SAKSLGGGFPIGAMLTT +IA  L++GTHG+TYGGN LASAVA AA++ I+TPEVL+
Sbjct: 247 ILTSAKSLGGGFPIGAMLTTDKIAPSLAIGTHGSTYGGNALASAVALAAVEHIDTPEVLE 306

Query: 310 GVKAKHERFKSRLQKIGQEYGIFDEIRGMGLLIGAALTDEWKGKARDVLNAAEKEAVMVL 369
           GV+ +H+ F+  L+ I +++G+F EIRGMGLL+GA ++D ++G+A+D+L  A +E VM L
Sbjct: 307 GVQKRHDLFREHLEAINEKHGVFKEIRGMGLLVGAQMSDAYEGRAKDILPLAIEEGVMAL 366

Query: 370 QASPDVVRFAPSLVIDDAEIDEGLERFERAVAKLV 404
            A P+V+R APSLVI +++IDEG+ R  RA+ +LV
Sbjct: 367 IAGPNVLRLAPSLVIPESDIDEGMTRLARAIDRLV 401


Lambda     K      H
   0.318    0.135    0.394 

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: 549
Number of extensions: 16
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: 406
Length of database: 404
Length adjustment: 31
Effective length of query: 375
Effective length of database: 373
Effective search space:   139875
Effective search space used:   139875
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_043529620.1 JH15_RS09230 (aspartate aminotransferase family 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.2993326.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.8e-213  694.7   0.0   2.1e-213  694.5   0.0    1.0  1  NCBI__GCF_000759345.1:WP_043529620.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000759345.1:WP_043529620.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  694.5   0.0  2.1e-213  2.1e-213       2     397 .]       6     401 ..       5     401 .. 1.00

  Alignments for each domain:
  == domain 1  score: 694.5 bits;  conditional E-value: 2.1e-213
                             TIGR03246   2 eresfdevmvpvyapakfipvrgeGsrvwdqegkeyidfaGGiavnalGhahpelvealkeqaeklwhlgngy 74 
                                           +r++fd++m p+y+p ++ipvrg+Gsr+wdqeg+eyidfaGGiavnalGh+hp lvealk q+e+lwhl+n+y
  NCBI__GCF_000759345.1:WP_043529620.1   6 TRSDFDQYMAPNYSPQQVIPVRGKGSRLWDQEGREYIDFAGGIAVNALGHCHPVLVEALKTQGETLWHLSNVY 78 
                                           699********************************************************************** PP

                             TIGR03246  75 tnepvlrlakklvdatfadkvffcnsGaeaneaalklarkvaldkygaekseivafknsfhGrtlftvsvGGq 147
                                           tnep+l+lak lv+ tfadkvf+c sG+eaneaalklar++ ++k+g++k++i++f++sfhGrt+ftvsvGGq
  NCBI__GCF_000759345.1:WP_043529620.1  79 TNEPALKLAKSLVERTFADKVFLCSSGGEANEAALKLARRYIYEKHGEQKDKIISFRQSFHGRTFFTVSVGGQ 151
                                           ************************************************************************* PP

                             TIGR03246 148 akysedfaplpegikhaayndlealkalisdktcavivepiqGegGvvpadkaflkglrelcdrhnallifde 220
                                           +kys++f+p+p+gi+ha+yndl++++ali+d+tca++vep+qGegG+vpa+++fl glrelcd+h+allifde
  NCBI__GCF_000759345.1:WP_043529620.1 152 PKYSQGFGPVPGGIQHAEYNDLDSVRALIDDNTCAIMVEPMQGEGGIVPATQEFLSGLRELCDQHQALLIFDE 224
                                           ************************************************************************* PP

                             TIGR03246 221 vqtGvGrtGelyaymeyGvtpdiltsakalGgGfpiGalltteelakvlkvGthGttyGGnplacavaekvld 293
                                           vqtGvGr G+++aym+yGvtpdiltsak+lGgGfpiGa+ltt+++a +l++GthG+tyGGn la+ava + ++
  NCBI__GCF_000759345.1:WP_043529620.1 225 VQTGVGRSGKFFAYMHYGVTPDILTSAKSLGGGFPIGAMLTTDKIAPSLAIGTHGSTYGGNALASAVALAAVE 297
                                           ************************************************************************* PP

                             TIGR03246 294 lvntaelleGvkqrhelfvdelekinarykvfseirGkGlliGavlteeyaGkakdlvnaaaeeGvlvliaGp 366
                                            ++t+e+leGv++rh+lf ++le+in+++ vf+eirG+Gll+Ga+++++y+G+akd++ +a eeGv++liaGp
  NCBI__GCF_000759345.1:WP_043529620.1 298 HIDTPEVLEGVQKRHDLFREHLEAINEKHGVFKEIRGMGLLVGAQMSDAYEGRAKDILPLAIEEGVMALIAGP 370
                                           ************************************************************************* PP

                             TIGR03246 367 dvvrfapslvieeeeikeGlarlekaveklv 397
                                           +v+r+apslvi+e++i+eG++rl++a+ +lv
  NCBI__GCF_000759345.1:WP_043529620.1 371 NVLRLAPSLVIPESDIDEGMTRLARAIDRLV 401
                                           ***************************9986 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 18.02
//
[ok]

This GapMind analysis is from Sep 24 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