Alignments for a candidate for astB in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for astB in Pseudomonas fluorescens FW300-N2E3

Align Succinylarginine dihydrolase (EC 3.5.3.23) (characterized)
to candidate AO353_03005 AO353_03005 succinylarginine dihydrolase

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



>FitnessBrowser__pseudo3_N2E3:AO353_03005
          Length = 448

 Score =  584 bits (1506), Expect = e-171
 Identities = 294/446 (65%), Positives = 346/446 (77%), Gaps = 3/446 (0%)

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

Query: 61  MLAPQERPDIHTLRRVGFTGSDADVLSQAAKASPVLLQACASASSMWTANAATVSPSADS 120
           +LAPQERPD+  LR +GF+G+DA V+ QAAK +  LL A  SASSMW ANAATVSPSAD+
Sbjct: 61  VLAPQERPDVGALRSLGFSGTDAQVIEQAAKQAMPLLVASCSASSMWVANAATVSPSADT 120

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

Query: 181 RLCHDYGQAGVEVFVYGRSVADLSRPAPVKYPARQTLEASQAVARLHQLSDDRTVYMQQN 240
           R C +YG+AGVE FV+GRS  D   PAP KYPARQTLEASQAVARLH LS+D  V+ QQN
Sbjct: 181 RFCREYGEAGVEFFVFGRSAFDTRYPAPQKYPARQTLEASQAVARLHGLSEDGVVFAQQN 240

Query: 241 PDVIDQGVFHNDVIAVGNQNVLFYHEQAFLETQAKLAEIDKKM---HGNMYFIEVPTAKV 297
           P VIDQGVFHNDVIAVGN   LFYHE AFL+T+  LAE+  K+    G    I VP ++V
Sbjct: 241 PSVIDQGVFHNDVIAVGNGEALFYHEDAFLDTEQMLAELSAKLAKRGGQFKAICVPRSQV 300

Query: 298 SVQDAVKSYLFNTQIITLSDGNMAIIAPTDCQENPAVHAYLNELVTLNTPIKAVHYFDVK 357
           SV+DAV+SYLFN+Q+++ +DG+M +I P +CQ NP V  YL EL +    I+ V  FD+K
Sbjct: 301 SVEDAVRSYLFNSQLLSRADGSMLLIVPQECQNNPRVWQYLQELTSSGGLIREVKVFDLK 360

Query: 358 QSMQNGGGPACLRLRVAMNETELAAVNPQVMMNDALFARLNQWVDKHYRDRLSTQDLADP 417
           QSMQNGGGPACLRLRVA+NETELAAVNP V+M   L+  L QWVDKHYRDR++  DLADP
Sbjct: 361 QSMQNGGGPACLRLRVALNETELAAVNPGVIMTPPLYGTLTQWVDKHYRDRMTESDLADP 420

Query: 418 QLLMESRTALDELTQIMKLGSVYQFQ 443
           QLL+E RTALDELTQI+KLG+VY FQ
Sbjct: 421 QLLLECRTALDELTQILKLGAVYPFQ 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: 552
Number of extensions: 19
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 AO353_03005 AO353_03005 (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.14332.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   7.1e-250  815.4   0.2     8e-250  815.2   0.2    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03005  AO353_03005 succinylarginine dih


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_03005  AO353_03005 succinylarginine dihydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  815.2   0.2    8e-250    8e-250       1     443 []       3     446 ..       3     446 .. 1.00

  Alignments for each domain:
  == domain 1  score: 815.2 bits;  conditional E-value: 8e-250
                                     TIGR03241   1 ayevnfdGlvGlthnyaGlsfGnkastsnkksvsnpklaakqGllkmkaladlGfkqgvlapqer 65 
                                                   +yevnfdGlvG+thny+Gls+Gn+as+sn+++ snpk+aa qGl+kmkal+++Gf+qgvlapqer
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03005   3 SYEVNFDGLVGPTHNYGGLSYGNVASQSNSQQSSNPKEAALQGLAKMKALMEMGFQQGVLAPQER 67 
                                                   69*************************************************************** PP

                                     TIGR03241  66 pdiaalrklGfsGsdeevlekaareapellsavssassmwtanaatvspsadtadgrvhftaanl 130
                                                   pd+ alr lGfsG d++v+e+aa++a+ ll+a++sassmw+anaatvspsadtadgrvhftaanl
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03005  68 PDVGALRSLGFSGTDAQVIEQAAKQAMPLLVASCSASSMWVANAATVSPSADTADGRVHFTAANL 132
                                                   ***************************************************************** PP

                                     TIGR03241 131 nnkfhrsieaettervlkaifadekkfavhealpavallGdeGaanhtrlgaeydepgvelfvyG 195
                                                   n+k+hrsie++tt+rvl a+fad+k+fa+h+alpava++GdeGaanhtr+++ey+e+gve+fv+G
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03005 133 NCKYHRSIEHPTTSRVLGAMFADQKHFAHHAALPAVAQFGDEGAANHTRFCREYGEAGVEFFVFG 197
                                                   ***************************************************************** PP

                                     TIGR03241 196 raal.erepkpkryparqtleasqavarlhqleeekvvyaqqnpdvidqGvfhndviavsnrevl 259
                                                   r+a+ +r+p+p++yparqtleasqavarlh+l+e+ vv+aqqnp+vidqGvfhndviav+n e l
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03005 198 RSAFdTRYPAPQKYPARQTLEASQAVARLHGLSEDGVVFAQQNPSVIDQGVFHNDVIAVGNGEAL 262
                                                   ****999********************************************************** PP

                                     TIGR03241 260 fhhekaflnqsqvldelraklaalgqelvaievpdaevsvedavssylfnsqllskedgkmllvv 324
                                                   f+he+afl+++q+l+el akla  g++++ai+vp+++vsvedav+sylfnsqlls++dg+mll+v
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03005 263 FYHEDAFLDTEQMLAELSAKLAKRGGQFKAICVPRSQVSVEDAVRSYLFNSQLLSRADGSMLLIV 327
                                                   ***************************************************************** PP

                                     TIGR03241 325 peecreneavwayldelvaadgpikevkvfdlresmknGGGpaclrlrvvlndaelaavnpkvll 389
                                                   p+ec++n++vw+yl+el++++g i+evkvfdl++sm+nGGGpaclrlrv+ln++elaavnp v++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03005 328 PQECQNNPRVWQYLQELTSSGGLIREVKVFDLKQSMQNGGGPACLRLRVALNETELAAVNPGVIM 392
                                                   ***************************************************************** PP

                                     TIGR03241 390 sdalfatlnkwvdrhyrdrlsakdladpqllvesrtaldeltqilnlGsvyefq 443
                                                   +  l+ tl++wvd+hyrdr++++dladpqll e+rtaldeltqil+lG+vy+fq
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03005 393 TPPLYGTLTQWVDKHYRDRMTESDLADPQLLLECRTALDELTQILKLGAVYPFQ 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.87
//
[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