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

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.16029.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.95
//
[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