GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astB in Pseudomonas fluorescens FW300-N2C3

Align Succinylarginine dihydrolase (EC 3.5.3.23) (characterized)
to candidate AO356_18745 AO356_18745 succinylarginine dihydrolase

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_18745
          Length = 448

 Score =  570 bits (1468), Expect = e-167
 Identities = 290/446 (65%), Positives = 337/446 (75%), Gaps = 3/446 (0%)

Query: 1   MKHFEANFDGLVGPTHNYAGLSFGNVASQSNAAQVSNPKDAAKQGLKKAKALADMGMVQG 60
           MK +E NFDGLVGPTHNY GLS+GNVASQSN+ Q SNPK+AA QGL K KAL DMG  QG
Sbjct: 1   MKSYEVNFDGLVGPTHNYGGLSYGNVASQSNSQQSSNPKEAALQGLAKMKALMDMGFQQG 60

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

Query: 121 DDGKLHFTPANLVDKLHRSIEPVTTGNILKAIFTDERYFAHHQHLPEHPHFGDEGAANHT 180
            DG++HFT ANL  K HRSIE  TT  +L A+F D+++FAHH  LP    FGDEGAANHT
Sbjct: 121 ADGRVHFTAANLNCKYHRSIEHPTTSRVLGAMFADQQHFAHHAALPAVAQFGDEGAANHT 180

Query: 181 RLCHDYGQAGVEVFVYGRSVADLSRPAPVKYPARQTLEASQAVARLHQLSDDRTVYMQQN 240
           R C  YG+AGVE FV+GRS  D   PAP KYPARQTLEASQAVARLH L ++  VY QQN
Sbjct: 181 RFCRAYGEAGVEFFVFGRSAFDTRYPAPQKYPARQTLEASQAVARLHGLREEGVVYAQQN 240

Query: 241 PDVIDQGVFHNDVIAVGNQNVLFYHEQAFLETQAKLAEIDKKM---HGNMYFIEVPTAKV 297
           P VIDQGVFHNDVIAVGN  VLFYHE AFLET   LAE+  K+    G    + VP + V
Sbjct: 241 PSVIDQGVFHNDVIAVGNGEVLFYHEDAFLETDRMLAELSSKLAKVGGKFQSVCVPRSAV 300

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

Query: 358 QSMQNGGGPACLRLRVAMNETELAAVNPQVMMNDALFARLNQWVDKHYRDRLSTQDLADP 417
           QSMQNGGGPACLRLRVA+NETELAAVNP V+M   L+  L QWV++HYRDR++  DLADP
Sbjct: 361 QSMQNGGGPACLRLRVALNETELAAVNPGVIMTAPLYDSLTQWVERHYRDRMTENDLADP 420

Query: 418 QLLMESRTALDELTQIMKLGSVYQFQ 443
           QLL+E R ALDELTQI+KLG+VY FQ
Sbjct: 421 QLLLECRAALDELTQILKLGAVYPFQ 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: 542
Number of extensions: 12
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: 448
Length adjustment: 32
Effective length of query: 412
Effective length of database: 416
Effective search space:   171392
Effective search space used:   171392
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 AO356_18745 AO356_18745 (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.16354.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   1.2e-248  811.4   0.3   1.3e-248  811.2   0.3    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18745  AO356_18745 succinylarginine dih


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18745  AO356_18745 succinylarginine dihydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  811.2   0.3  1.3e-248  1.3e-248       1     443 []       3     446 ..       3     446 .. 1.00

  Alignments for each domain:
  == domain 1  score: 811.2 bits;  conditional E-value: 1.3e-248
                                       TIGR03241   1 ayevnfdGlvGlthnyaGlsfGnkastsnkksvsnpklaakqGllkmkaladlGfkqgvlapq 63 
                                                     +yevnfdGlvG+thny+Gls+Gn+as+sn+++ snpk+aa qGl+kmkal+d+Gf+qgvlapq
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18745   3 SYEVNFDGLVGPTHNYGGLSYGNVASQSNSQQSSNPKEAALQGLAKMKALMDMGFQQGVLAPQ 65 
                                                     69************************************************************* PP

                                       TIGR03241  64 erpdiaalrklGfsGsdeevlekaareapellsavssassmwtanaatvspsadtadgrvhft 126
                                                     erpd+aalr+lGf+Gsd++v+++aa+ea+ ll+a++sassmw+anaatvspsadtadgrvhft
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18745  66 ERPDVAALRRLGFAGSDAQVIQQAAKEAMPLLVASCSASSMWVANAATVSPSADTADGRVHFT 128
                                                     *************************************************************** PP

                                       TIGR03241 127 aanlnnkfhrsieaettervlkaifadekkfavhealpavallGdeGaanhtrlgaeydepgv 189
                                                     aanln+k+hrsie++tt+rvl a+fad+++fa+h+alpava++GdeGaanhtr++++y+e+gv
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18745 129 AANLNCKYHRSIEHPTTSRVLGAMFADQQHFAHHAALPAVAQFGDEGAANHTRFCRAYGEAGV 191
                                                     *************************************************************** PP

                                       TIGR03241 190 elfvyGraal.erepkpkryparqtleasqavarlhqleeekvvyaqqnpdvidqGvfhndvi 251
                                                     e+fv+Gr+a+ +r+p+p++yparqtleasqavarlh+l+ee vvyaqqnp+vidqGvfhndvi
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18745 192 EFFVFGRSAFdTRYPAPQKYPARQTLEASQAVARLHGLREEGVVYAQQNPSVIDQGVFHNDVI 254
                                                     **********999************************************************** PP

                                       TIGR03241 252 avsnrevlfhhekaflnqsqvldelraklaalgqelvaievpdaevsvedavssylfnsqlls 314
                                                     av+n evlf+he+afl+++ +l+el +kla +g+++++++vp+++v+v+dav+sylfnsqlls
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18745 255 AVGNGEVLFYHEDAFLETDRMLAELSSKLAKVGGKFQSVCVPRSAVTVDDAVRSYLFNSQLLS 317
                                                     *************************************************************** PP

                                       TIGR03241 315 kedgkmllvvpeecreneavwayldelvaadgpikevkvfdlresmknGGGpaclrlrvvlnd 377
                                                     + dg+mll+vpeecr ne+vw+yl+ l+ a+g i+evkvfdl++sm+nGGGpaclrlrv+ln+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18745 318 RPDGSMLLIVPEECRGNERVWQYLQGLTGAGGVIREVKVFDLKQSMQNGGGPACLRLRVALNE 380
                                                     *************************************************************** PP

                                       TIGR03241 378 aelaavnpkvllsdalfatlnkwvdrhyrdrlsakdladpqllvesrtaldeltqilnlGsvy 440
                                                     +elaavnp v++++ l+++l++wv+rhyrdr++++dladpqll e+r aldeltqil+lG+vy
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18745 381 TELAAVNPGVIMTAPLYDSLTQWVERHYRDRMTENDLADPQLLLECRAALDELTQILKLGAVY 443
                                                     *************************************************************** PP

                                       TIGR03241 441 efq 443
                                                     +fq
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18745 444 PFQ 446
                                                     **9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (443 nodes)
Target sequences:                          1  (448 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.75
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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