Alignments for a candidate for astB in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for astB in Pseudomonas putida KT2440

Align Succinylarginine dihydrolase (EC 3.5.3.23) (characterized)
to candidate PP_4477 PP_4477 N-succinylarginine dihydrolase

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



>FitnessBrowser__Putida:PP_4477
          Length = 449

 Score =  588 bits (1517), Expect = e-173
 Identities = 298/447 (66%), Positives = 346/447 (77%), Gaps = 3/447 (0%)

Query: 1   MKHFEANFDGLVGPTHNYAGLSFGNVASQSNAAQVSNPKDAAKQGLKKAKALADMGMVQG 60
           MK +E NFDGLVGPTHNY GLS+GNVASQSN+ Q SNP++AA+QGL K KALADMG  QG
Sbjct: 1   MKSYEVNFDGLVGPTHNYGGLSYGNVASQSNSQQASNPREAARQGLAKMKALADMGFKQG 60

Query: 61  MLAPQERPDIHTLRRVGFTGSDADVLSQAAKASPVLLQACASASSMWTANAATVSPSADS 120
           +LAPQERPD+  LRR+GF+GSDA+V+ +AA+ +  LL A  SASSMW ANAATVSPSAD+
Sbjct: 61  VLAPQERPDVAALRRLGFSGSDAEVIQRAAREAMPLLVASCSASSMWVANAATVSPSADT 120

Query: 121 DDGKLHFTPANLVDKLHRSIEPVTTGNILKAIFTDERYFAHHQHLPEHPHFGDEGAANHT 180
            DG++HFT ANL  K HRSIE  TT  +L A+F DE+YFAHH  LP    FGDEGAANHT
Sbjct: 121 ADGRVHFTAANLNCKYHRSIEHPTTSRVLGAMFNDEKYFAHHAALPAVAQFGDEGAANHT 180

Query: 181 RLCHDYGQAGVEVFVYGRSVADLSRPAPVKYPARQTLEASQAVARLHQLSDDRTVYMQQN 240
           R C  YG+AGVE FVYGRS  D   PAP KYPARQTLEASQAVARLH LSDD  VY QQN
Sbjct: 181 RFCRAYGEAGVEFFVYGRSAFDSRYPAPQKYPARQTLEASQAVARLHGLSDDGVVYAQQN 240

Query: 241 PDVIDQGVFHNDVIAVGNQNVLFYHEQAFLETQAKLAEIDKKM---HGNMYFIEVPTAKV 297
           P VIDQGVFHNDVI+VGN  VLFYHE AFLET A L ++  K+    GN   I VP A V
Sbjct: 241 PAVIDQGVFHNDVISVGNGEVLFYHEDAFLETDAVLGQLRAKLASKGGNFQAICVPRAAV 300

Query: 298 SVQDAVKSYLFNTQIITLSDGNMAIIAPTDCQENPAVHAYLNELVTLNTPIKAVHYFDVK 357
           +V+DAV+SYLFN+Q+++  DG+M ++ P +C+ N  V AYL +L +   P+K V  FD+K
Sbjct: 301 AVEDAVRSYLFNSQLLSREDGSMLLVVPEECRNNERVWAYLGQLTSQGGPVKEVKVFDLK 360

Query: 358 QSMQNGGGPACLRLRVAMNETELAAVNPQVMMNDALFARLNQWVDKHYRDRLSTQDLADP 417
           QSMQNGGGPACLRLRVA+ E ELAAVN  V+M   L+  L QWVD+HYRDRL   DLADP
Sbjct: 361 QSMQNGGGPACLRLRVALKEAELAAVNQGVIMTATLYDTLLQWVDRHYRDRLGEADLADP 420

Query: 418 QLLMESRTALDELTQIMKLGSVYQFQR 444
           QLL+E RTALDELTQI+KLGSVY FQR
Sbjct: 421 QLLVECRTALDELTQILKLGSVYPFQR 447


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: 551
Number of extensions: 16
Number of successful extensions: 2
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: 449
Length adjustment: 33
Effective length of query: 411
Effective length of database: 416
Effective search space:   170976
Effective search space used:   170976
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 PP_4477 PP_4477 (N-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.21799.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   2.3e-258  843.4   0.5   2.6e-258  843.2   0.5    1.0  1  lcl|FitnessBrowser__Putida:PP_4477  PP_4477 N-succinylarginine dihyd


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_4477  PP_4477 N-succinylarginine dihydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  843.2   0.5  2.6e-258  2.6e-258       1     443 []       3     446 ..       3     446 .. 1.00

  Alignments for each domain:
  == domain 1  score: 843.2 bits;  conditional E-value: 2.6e-258
                           TIGR03241   1 ayevnfdGlvGlthnyaGlsfGnkastsnkksvsnpklaakqGllkmkaladlGfkqgvlapqerpdiaalrklG 75 
                                         +yevnfdGlvG+thny+Gls+Gn+as+sn++++snp++aa+qGl+kmkalad+Gfkqgvlapqerpd+aalr+lG
  lcl|FitnessBrowser__Putida:PP_4477   3 SYEVNFDGLVGPTHNYGGLSYGNVASQSNSQQASNPREAARQGLAKMKALADMGFKQGVLAPQERPDVAALRRLG 77 
                                         69************************************************************************* PP

                           TIGR03241  76 fsGsdeevlekaareapellsavssassmwtanaatvspsadtadgrvhftaanlnnkfhrsieaettervlkai 150
                                         fsGsd+ev+++aarea+ ll+a++sassmw+anaatvspsadtadgrvhftaanln+k+hrsie++tt+rvl a+
  lcl|FitnessBrowser__Putida:PP_4477  78 FSGSDAEVIQRAAREAMPLLVASCSASSMWVANAATVSPSADTADGRVHFTAANLNCKYHRSIEHPTTSRVLGAM 152
                                         *************************************************************************** PP

                           TIGR03241 151 fadekkfavhealpavallGdeGaanhtrlgaeydepgvelfvyGraal.erepkpkryparqtleasqavarlh 224
                                         f+dek+fa+h+alpava++GdeGaanhtr++++y+e+gve+fvyGr+a+ +r+p+p++yparqtleasqavarlh
  lcl|FitnessBrowser__Putida:PP_4477 153 FNDEKYFAHHAALPAVAQFGDEGAANHTRFCRAYGEAGVEFFVYGRSAFdSRYPAPQKYPARQTLEASQAVARLH 227
                                         *************************************************999*********************** PP

                           TIGR03241 225 qleeekvvyaqqnpdvidqGvfhndviavsnrevlfhhekaflnqsqvldelraklaalgqelvaievpdaevsv 299
                                         +l+++ vvyaqqnp+vidqGvfhndvi+v+n evlf+he+afl++++vl +lrakla++g++++ai+vp+a+v+v
  lcl|FitnessBrowser__Putida:PP_4477 228 GLSDDGVVYAQQNPAVIDQGVFHNDVISVGNGEVLFYHEDAFLETDAVLGQLRAKLASKGGNFQAICVPRAAVAV 302
                                         *************************************************************************** PP

                           TIGR03241 300 edavssylfnsqllskedgkmllvvpeecreneavwayldelvaadgpikevkvfdlresmknGGGpaclrlrvv 374
                                         edav+sylfnsqlls+edg+mllvvpeecr+ne+vwayl +l++++gp+kevkvfdl++sm+nGGGpaclrlrv+
  lcl|FitnessBrowser__Putida:PP_4477 303 EDAVRSYLFNSQLLSREDGSMLLVVPEECRNNERVWAYLGQLTSQGGPVKEVKVFDLKQSMQNGGGPACLRLRVA 377
                                         *************************************************************************** PP

                           TIGR03241 375 lndaelaavnpkvllsdalfatlnkwvdrhyrdrlsakdladpqllvesrtaldeltqilnlGsvyefq 443
                                         l++aelaavn+ v+++++l++tl +wvdrhyrdrl ++dladpqllve+rtaldeltqil+lGsvy+fq
  lcl|FitnessBrowser__Putida:PP_4477 378 LKEAELAAVNQGVIMTATLYDTLLQWVDRHYRDRLGEADLADPQLLVECRTALDELTQILKLGSVYPFQ 446
                                         ********************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (443 nodes)
Target sequences:                          1  (449 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.54
//
[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