Alignments for a candidate for astC in Halomonas xinjiangensis TRM 0175

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.3004541.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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 22.43
//
[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:

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 2024 update 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