Alignments for a candidate for astB in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for astB in Pseudomonas fluorescens GW456-L13

Align Succinylarginine dihydrolase (EC 3.5.3.23) (characterized)
to candidate PfGW456L13_1975 Succinylarginine dihydrolase (EC 3.5.3.23)

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1975
          Length = 448

 Score =  577 bits (1488), Expect = e-169
 Identities = 292/446 (65%), Positives = 343/446 (76%), 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+  LRR+GF G+DA V+ +AAK +  LL A  SASSMW ANAATVSPSAD+
Sbjct: 61  VLAPQERPDVAALRRLGFGGTDAQVIERAAKEAMPLLVASCSASSMWVANAATVSPSADT 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 LSDD  VY QQN
Sbjct: 181 RFCREYGEAGVEFFVFGRSAFDTRYPAPQKYPARQTLEASQAVARLHGLSDDGVVYAQQN 240

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

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

Query: 358 QSMQNGGGPACLRLRVAMNETELAAVNPQVMMNDALFARLNQWVDKHYRDRLSTQDLADP 417
           QSMQNGGGPACLRLRVA+NETELAAVNP V+M   L+  L +WV+KHYRDR++  DLADP
Sbjct: 361 QSMQNGGGPACLRLRVALNETELAAVNPGVIMTAPLYGTLTEWVEKHYRDRMTENDLADP 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: 554
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: 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 PfGW456L13_1975 (Succinylarginine dihydrolase (EC 3.5.3.23))
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.27515.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   1.1e-248  811.5   0.1   1.2e-248  811.3   0.1    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1975  Succinylarginine dihydrolase (EC


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1975  Succinylarginine dihydrolase (EC 3.5.3.23)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  811.3   0.1  1.2e-248  1.2e-248       1     443 []       3     446 ..       3     446 .. 1.00

  Alignments for each domain:
  == domain 1  score: 811.3 bits;  conditional E-value: 1.2e-248
                                               TIGR03241   1 ayevnfdGlvGlthnyaGlsfGnkastsnkksvsnpklaakqGllkmkaladlGf 55 
                                                             +yevnfdGlvG+thny+Gls+Gn+as+sn+++ snpk+aa qGl+kmkal+++Gf
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1975   3 SYEVNFDGLVGPTHNYGGLSYGNVASQSNSQQSSNPKEAALQGLAKMKALMEMGF 57 
                                                             69***************************************************** PP

                                               TIGR03241  56 kqgvlapqerpdiaalrklGfsGsdeevlekaareapellsavssassmwtanaa 110
                                                             +qgvlapqerpd+aalr+lGf+G d++v+e+aa+ea+ ll+a++sassmw+anaa
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1975  58 QQGVLAPQERPDVAALRRLGFGGTDAQVIERAAKEAMPLLVASCSASSMWVANAA 112
                                                             ******************************************************* PP

                                               TIGR03241 111 tvspsadtadgrvhftaanlnnkfhrsieaettervlkaifadekkfavhealpa 165
                                                             tvspsadtadgrvhftaanln+k+hrsie++tt+rvl a+fad+k+fa+h+alpa
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1975 113 TVSPSADTADGRVHFTAANLNCKYHRSIEHPTTSRVLGAMFADQKHFAHHAALPA 167
                                                             ******************************************************* PP

                                               TIGR03241 166 vallGdeGaanhtrlgaeydepgvelfvyGraal.erepkpkryparqtleasqa 219
                                                             va++GdeGaanhtr+++ey+e+gve+fv+Gr+a+ +r+p+p++yparqtleasqa
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1975 168 VAQFGDEGAANHTRFCREYGEAGVEFFVFGRSAFdTRYPAPQKYPARQTLEASQA 222
                                                             **********************************999****************** PP

                                               TIGR03241 220 varlhqleeekvvyaqqnpdvidqGvfhndviavsnrevlfhhekaflnqsqvld 274
                                                             varlh+l+++ vvyaqqnp+vidqGvfhndviav+n evlf+he+afl+++++l+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1975 223 VARLHGLSDDGVVYAQQNPSVIDQGVFHNDVIAVGNGEVLFYHEDAFLETEKMLA 277
                                                             ******************************************************* PP

                                               TIGR03241 275 elraklaalgqelvaievpdaevsvedavssylfnsqllskedgkmllvvpeecr 329
                                                             el++kla +g+++++++vp+++vsvedav+sylfnsqlls+ dg+mll+vpeecr
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1975 278 ELQSKLAKVGGKFQSVCVPRSAVSVEDAVRSYLFNSQLLSRPDGSMLLIVPEECR 332
                                                             ******************************************************* PP

                                               TIGR03241 330 eneavwayldelvaadgpikevkvfdlresmknGGGpaclrlrvvlndaelaavn 384
                                                              ne+vw+yl+ l++++g i+evkvfdl++sm+nGGGpaclrlrv+ln++elaavn
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1975 333 GNERVWQYLQGLTSSGGLIREVKVFDLKQSMQNGGGPACLRLRVALNETELAAVN 387
                                                             ******************************************************* PP

                                               TIGR03241 385 pkvllsdalfatlnkwvdrhyrdrlsakdladpqllvesrtaldeltqilnlGsv 439
                                                             p v++++ l+ tl++wv++hyrdr++++dladpqll e+rtaldeltqil+lG+v
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1975 388 PGVIMTAPLYGTLTEWVEKHYRDRMTENDLADPQLLLECRTALDELTQILKLGAV 442
                                                             ******************************************************* PP

                                               TIGR03241 440 yefq 443
                                                             y+fq
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1975 443 YPFQ 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: 9.42
//
[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