Alignments for a candidate for astC in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for astC in Burkholderia phytofirmans PsJN

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate BPHYT_RS07695 BPHYT_RS07695 acetylornithine aminotransferase

Query= reanno::WCS417:GFF4238
         (406 letters)



>FitnessBrowser__BFirm:BPHYT_RS07695
          Length = 411

 Score =  508 bits (1309), Expect = e-148
 Identities = 240/399 (60%), Positives = 311/399 (77%)

Query: 8   VQRADFDQVMVPNYAPAAFIPVRGEGSRVWDQAGRELIDFAGGIAVNVLGHAHPALVGAL 67
           V R  FD+VMVP ++PAAF+P RG GSRVWD  GR+ IDFAGGIAV  LGHAHP L+  L
Sbjct: 6   VTRQTFDEVMVPVFSPAAFVPDRGLGSRVWDTQGRDYIDFAGGIAVTALGHAHPELLNVL 65

Query: 68  TEQAHKLWHVSNVFTNEPALRLAHKLIDATFAERVFFCNSGAEANEAAFKLARRVAFDRF 127
            EQ  KLWH+ N +TNEP LRLA +L D TFA+R FF NSGAEANEAA KLARRVAFDR 
Sbjct: 66  HEQGGKLWHIGNGYTNEPVLRLAKRLEDLTFADRAFFANSGAEANEAALKLARRVAFDRH 125

Query: 128 GSEKYEIIAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLDALKAAVSDKT 187
           G++KYEII+   SFHGRT FTV+VGGQ KYS+GFGP   GITH+PYND++A+K A+  +T
Sbjct: 126 GADKYEIISFTQSFHGRTFFTVSVGGQPKYSEGFGPVPAGITHLPYNDIEAVKKAIGAQT 185

Query: 188 CAVVLEPIQGEGGVLPAELAYLQGARDLCDANNALLVFDEVQTGMGRSGHLFAYQHYGVT 247
           CAV++EPIQGEGGV+PA+ A+L+  R+ CD + ALL+FDEVQTG+GRSG+ +AYQ  GVT
Sbjct: 186 CAVIVEPIQGEGGVIPADPAFLKALREACDQHGALLIFDEVQTGVGRSGYFYAYQETGVT 245

Query: 248 PDILTSAKSLGGGFPIAAMLTTEALAKHLVVGTHGTTYGGNPLACAVAEAVIDVINTPEV 307
           PDILT+AK+LG GFPI AMLTT  LA +  VG HGTTYGGNPL  A+AE V+++++ P++
Sbjct: 246 PDILTTAKALGNGFPIGAMLTTNELAAYFKVGVHGTTYGGNPLGAAIAEKVVELVSDPKL 305

Query: 308 LAGVNAKHDLFKARLEQIGKQYGIFTEVRGMGLLLGCVLSDAFKGKAKDVFNAAEKENLM 367
           L GV ++ +  K  L ++ +++G+FTEVRG GLL+G  L++AFKG+AKD   AA +  ++
Sbjct: 306 LEGVRSRSEALKGHLAKLNERFGLFTEVRGRGLLIGAELNEAFKGRAKDFVTAAGQHGVI 365

Query: 368 ILQAGPDVVRFAPSLVVEDADIKEGLDRFERAVKALTQA 406
           +L AGPDV+RF PSL++   D+ EG +R  +A++++  A
Sbjct: 366 MLMAGPDVLRFVPSLIMPLDDMNEGFERLAKAIESIVGA 404


Lambda     K      H
   0.320    0.137    0.400 

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: 536
Number of extensions: 15
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: 411
Length adjustment: 31
Effective length of query: 375
Effective length of database: 380
Effective search space:   142500
Effective search space used:   142500
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 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate BPHYT_RS07695 BPHYT_RS07695 (acetylornithine aminotransferase)
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.8576.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   2.6e-215  700.8   0.1   2.9e-215  700.6   0.1    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS07695  BPHYT_RS07695 acetylornithine am


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS07695  BPHYT_RS07695 acetylornithine aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  700.6   0.1  2.9e-215  2.9e-215       1     397 []       6     402 ..       6     402 .. 1.00

  Alignments for each domain:
  == domain 1  score: 700.6 bits;  conditional E-value: 2.9e-215
                                TIGR03246   1 veresfdevmvpvyapakfipvrgeGsrvwdqegkeyidfaGGiavnalGhahpelvealkeqaeklwhl 70 
                                              v+r++fdevmvpv++pa+f+p+rg Gsrvwd++g++yidfaGGiav+alGhahpel ++l+eq+ klwh+
  lcl|FitnessBrowser__BFirm:BPHYT_RS07695   6 VTRQTFDEVMVPVFSPAAFVPDRGLGSRVWDTQGRDYIDFAGGIAVTALGHAHPELLNVLHEQGGKLWHI 75 
                                              79******************************************************************** PP

                                TIGR03246  71 gngytnepvlrlakklvdatfadkvffcnsGaeaneaalklarkvaldkygaekseivafknsfhGrtlf 140
                                              gngytnepvlrlak+l d tfad++ff+nsGaeaneaalklar+va+d++ga+k+ei++f++sfhGrt+f
  lcl|FitnessBrowser__BFirm:BPHYT_RS07695  76 GNGYTNEPVLRLAKRLEDLTFADRAFFANSGAEANEAALKLARRVAFDRHGADKYEIISFTQSFHGRTFF 145
                                              ********************************************************************** PP

                                TIGR03246 141 tvsvGGqakysedfaplpegikhaayndlealkalisdktcavivepiqGegGvvpadkaflkglrelcd 210
                                              tvsvGGq+kyse+f+p+p+gi+h++ynd+ea+k++i  +tcavivepiqGegGv+pad+aflk+lre+cd
  lcl|FitnessBrowser__BFirm:BPHYT_RS07695 146 TVSVGGQPKYSEGFGPVPAGITHLPYNDIEAVKKAIGAQTCAVIVEPIQGEGGVIPADPAFLKALREACD 215
                                              ********************************************************************** PP

                                TIGR03246 211 rhnallifdevqtGvGrtGelyaymeyGvtpdiltsakalGgGfpiGalltteelakvlkvGthGttyGG 280
                                              +h+allifdevqtGvGr G++yay+e+Gvtpdilt+akalG+GfpiGa+ltt+ela+ +kvG+hGttyGG
  lcl|FitnessBrowser__BFirm:BPHYT_RS07695 216 QHGALLIFDEVQTGVGRSGYFYAYQETGVTPDILTTAKALGNGFPIGAMLTTNELAAYFKVGVHGTTYGG 285
                                              ********************************************************************** PP

                                TIGR03246 281 nplacavaekvldlvntaelleGvkqrhelfvdelekinarykvfseirGkGlliGavlteeyaGkakdl 350
                                              npl++a+aekv++lv++++lleGv+ r+e +  +l+k+n+r+ +f+e+rG+GlliGa+l+e+++G+akd+
  lcl|FitnessBrowser__BFirm:BPHYT_RS07695 286 NPLGAAIAEKVVELVSDPKLLEGVRSRSEALKGHLAKLNERFGLFTEVRGRGLLIGAELNEAFKGRAKDF 355
                                              ********************************************************************** PP

                                TIGR03246 351 vnaaaeeGvlvliaGpdvvrfapslvieeeeikeGlarlekaveklv 397
                                              v+aa ++Gv++l+aGpdv+rf psl+++ ++++eG++rl+ka+e++v
  lcl|FitnessBrowser__BFirm:BPHYT_RS07695 356 VTAAGQHGVIMLMAGPDVLRFVPSLIMPLDDMNEGFERLAKAIESIV 402
                                              *******************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (397 nodes)
Target sequences:                          1  (411 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.13
//
[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:

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 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