GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astB in Paraburkholderia bryophila 376MFSha3.1

Align Succinylarginine dihydrolase (EC 3.5.3.23) (characterized)
to candidate H281DRAFT_06482 H281DRAFT_06482 succinylarginine dihydrolase

Query= reanno::SB2B:6937151
         (444 letters)



>FitnessBrowser__Burk376:H281DRAFT_06482
          Length = 446

 Score =  536 bits (1382), Expect = e-157
 Identities = 273/447 (61%), Positives = 334/447 (74%), Gaps = 4/447 (0%)

Query: 1   MKHFEANFDGLVGPTHNYAGLSFGNVASQSNAAQVSNPKDAAKQGLKKAKALADMGMVQG 60
           M+  EANFDGLVGPTHNYAGLSFGNVASQ+N   V+NPK AAKQGL+K K LAD+G  QG
Sbjct: 1   MQATEANFDGLVGPTHNYAGLSFGNVASQNNEKSVANPKAAAKQGLRKMKQLADLGFHQG 60

Query: 61  MLAPQERPDIHTLRRVGFTGSDADVLSQAAKASPVLLQACASASSMWTANAATVSPSADS 120
           +L PQERP +  LR +GF+G DA V+++ AK +P LL A +SAS+MWTANAATVSPSAD+
Sbjct: 61  VLPPQERPSMRLLRELGFSGDDATVIARVAKNAPELLAAASSASAMWTANAATVSPSADT 120

Query: 121 DDGKLHFTPANLVDKLHRSIEPVTTGNILKAIFTDERYFAHHQHLPEHPHFGDEGAANHT 180
            DG++HFTPANL  KLHR+IE  +T   L+AIF+D   FA H+ LP  P  GDEGAANHT
Sbjct: 121 HDGRVHFTPANLCSKLHRAIEHESTRRTLRAIFSDADRFAVHEALPGTPALGDEGAANHT 180

Query: 181 RLCHDYGQAGVEVFVYGRSVADLSRPAPVKYPARQTLEASQAVARLHQLSDDRTVYMQQN 240
           R C +YG  GVE FVYGRS      P P ++PARQT EAS+AVA  H L D+ TVY QQN
Sbjct: 181 RFCSEYGTRGVEFFVYGRSEYRRG-PEPKRFPARQTFEASRAVAHRHGLLDEATVYAQQN 239

Query: 241 PDVIDQGVFHNDVIAVGNQNVLFYHEQAFLETQAKLAEIDKKMHG---NMYFIEVPTAKV 297
           P+VID GVFHNDVIAVGN+N LF HE AF+E  A   E+  K+ G       IEVP A+V
Sbjct: 240 PEVIDAGVFHNDVIAVGNRNTLFCHELAFVEQNAVYDELRAKLAGLKAQFNVIEVPDAQV 299

Query: 298 SVQDAVKSYLFNTQIITLSDGNMAIIAPTDCQENPAVHAYLNELVTLNTPIKAVHYFDVK 357
           SV DAV SYLFN+Q++T  DG   ++ P +C+ENP V AYL++L +   PI  V  FD++
Sbjct: 300 SVADAVSSYLFNSQLLTRPDGKQVLVVPQECRENPRVAAYLDDLTSHTGPIDDVLVFDLR 359

Query: 358 QSMQNGGGPACLRLRVAMNETELAAVNPQVMMNDALFARLNQWVDKHYRDRLSTQDLADP 417
           +SM+NGGGPACLRLRV +++ E AAV   V ++D LF RL+ W++KHYRDRL+  DL DP
Sbjct: 360 ESMKNGGGPACLRLRVVLSDAERAAVTQGVWIDDTLFGRLDSWIEKHYRDRLAPADLTDP 419

Query: 418 QLLMESRTALDELTQIMKLGSVYQFQR 444
           QLL+ESR+ALDELTQI+ LGS+Y FQR
Sbjct: 420 QLLVESRSALDELTQILGLGSLYDFQR 446


Lambda     K      H
   0.318    0.131    0.380 

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: 17
Number of successful extensions: 3
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: 444
Length of database: 446
Length adjustment: 32
Effective length of query: 412
Effective length of database: 414
Effective search space:   170568
Effective search space used:   170568
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: 51 (24.3 bits)

Align candidate H281DRAFT_06482 H281DRAFT_06482 (succinylarginine dihydrolase)
to HMM TIGR03241 (astB: succinylarginine dihydrolase (EC 3.5.3.23))

# 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/TIGR03241.hmm
# target sequence database:        /tmp/gapView.555817.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03241  [M=443]
Accession:   TIGR03241
Description: arg_catab_astB: succinylarginine dihydrolase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
     2e-243  794.1   0.1   2.3e-243  793.9   0.1    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_06482  H281DRAFT_06482 succinylarginine


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_06482  H281DRAFT_06482 succinylarginine dihydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  793.9   0.1  2.3e-243  2.3e-243       1     443 []       3     445 ..       3     445 .. 1.00

  Alignments for each domain:
  == domain 1  score: 793.9 bits;  conditional E-value: 2.3e-243
                                    TIGR03241   1 ayevnfdGlvGlthnyaGlsfGnkastsnkksvsnpklaakqGllkmkaladlGfkqgvlapqerp 66 
                                                  a e+nfdGlvG+thnyaGlsfGn+as++n+ksv+npk+aakqGl+kmk+ladlGf+qgvl+pqerp
  lcl|FitnessBrowser__Burk376:H281DRAFT_06482   3 ATEANFDGLVGPTHNYAGLSFGNVASQNNEKSVANPKAAAKQGLRKMKQLADLGFHQGVLPPQERP 68 
                                                  579*************************************************************** PP

                                    TIGR03241  67 diaalrklGfsGsdeevlekaareapellsavssassmwtanaatvspsadtadgrvhftaanlnn 132
                                                  +++ lr+lGfsG+d+ v++++a++apell+a+ssas+mwtanaatvspsadt dgrvhft+anl++
  lcl|FitnessBrowser__Burk376:H281DRAFT_06482  69 SMRLLRELGFSGDDATVIARVAKNAPELLAAASSASAMWTANAATVSPSADTHDGRVHFTPANLCS 134
                                                  ****************************************************************** PP

                                    TIGR03241 133 kfhrsieaettervlkaifadekkfavhealpavallGdeGaanhtrlgaeydepgvelfvyGraa 198
                                                  k+hr+ie+e+t+r+l+aif+d ++favhealp + +lGdeGaanhtr+++ey+  gve+fvyGr++
  lcl|FitnessBrowser__Burk376:H281DRAFT_06482 135 KLHRAIEHESTRRTLRAIFSDADRFAVHEALPGTPALGDEGAANHTRFCSEYGTRGVEFFVYGRSE 200
                                                  ****************************************************************** PP

                                    TIGR03241 199 lerepkpkryparqtleasqavarlhqleeekvvyaqqnpdvidqGvfhndviavsnrevlfhhek 264
                                                  ++r+p+pkr+parqt+eas+ava++h+l +e++vyaqqnp+vid+Gvfhndviav+nr++lf+he 
  lcl|FitnessBrowser__Burk376:H281DRAFT_06482 201 YRRGPEPKRFPARQTFEASRAVAHRHGLLDEATVYAQQNPEVIDAGVFHNDVIAVGNRNTLFCHEL 266
                                                  ****************************************************************** PP

                                    TIGR03241 265 aflnqsqvldelraklaalgqelvaievpdaevsvedavssylfnsqllskedgkmllvvpeecre 330
                                                  af++q++v+delrakla+l++++++ievpda+vsv+davssylfnsqll++ dgk++lvvp+ecre
  lcl|FitnessBrowser__Burk376:H281DRAFT_06482 267 AFVEQNAVYDELRAKLAGLKAQFNVIEVPDAQVSVADAVSSYLFNSQLLTRPDGKQVLVVPQECRE 332
                                                  ****************************************************************** PP

                                    TIGR03241 331 neavwayldelvaadgpikevkvfdlresmknGGGpaclrlrvvlndaelaavnpkvllsdalfat 396
                                                  n++v+ayld+l+++ gpi++v vfdlresmknGGGpaclrlrvvl+dae+aav + v+++d+lf +
  lcl|FitnessBrowser__Burk376:H281DRAFT_06482 333 NPRVAAYLDDLTSHTGPIDDVLVFDLRESMKNGGGPACLRLRVVLSDAERAAVTQGVWIDDTLFGR 398
                                                  ****************************************************************** PP

                                    TIGR03241 397 lnkwvdrhyrdrlsakdladpqllvesrtaldeltqilnlGsvyefq 443
                                                  l++w+++hyrdrl+ +dl+dpqllvesr+aldeltqil+lGs+y+fq
  lcl|FitnessBrowser__Burk376:H281DRAFT_06482 399 LDSWIEKHYRDRLAPADLTDPQLLVESRSALDELTQILGLGSLYDFQ 445
                                                  **********************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (443 nodes)
Target sequences:                          1  (446 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: 22.20
//
[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