Alignments for a candidate for astB in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for astB in Shewanella oneidensis MR-1

Align Succinylarginine dihydrolase (EC 3.5.3.23) (characterized)
to candidate 201844 SO2706 succinylarginine dihydrolase (NCBI ptt file)

Query= reanno::MR1:201844
         (444 letters)



>FitnessBrowser__MR1:201844
          Length = 444

 Score =  893 bits (2308), Expect = 0.0
 Identities = 444/444 (100%), Positives = 444/444 (100%)

Query: 1   MKHFEANFDGLVGPTHNYAGLSFGNVASLNNAALVSNPKAAAKQGLQKAKALADLGMIQG 60
           MKHFEANFDGLVGPTHNYAGLSFGNVASLNNAALVSNPKAAAKQGLQKAKALADLGMIQG
Sbjct: 1   MKHFEANFDGLVGPTHNYAGLSFGNVASLNNAALVSNPKAAAKQGLQKAKALADLGMIQG 60

Query: 61  MLAPQERPDLNTLRRIGFSGSDAQVLQQAAKTAPALLNACCSASSMWTANAATVSPSADT 120
           MLAPQERPDLNTLRRIGFSGSDAQVLQQAAKTAPALLNACCSASSMWTANAATVSPSADT
Sbjct: 61  MLAPQERPDLNTLRRIGFSGSDAQVLQQAAKTAPALLNACCSASSMWTANAATVSPSADT 120

Query: 121 RDGKLHFTPANLVDKLHRSIEPITTGRILTATFNDPHYFYHHNHLPEHNSFGDEGAANHT 180
           RDGKLHFTPANLVDKLHRSIEPITTGRILTATFNDPHYFYHHNHLPEHNSFGDEGAANHT
Sbjct: 121 RDGKLHFTPANLVDKLHRSIEPITTGRILTATFNDPHYFYHHNHLPEHNSFGDEGAANHT 180

Query: 181 RLCQEYGHAGVELFVYGQEATNPHAPKPLKFPARQTLEASMAIARLHQLEEDNCVFIQQN 240
           RLCQEYGHAGVELFVYGQEATNPHAPKPLKFPARQTLEASMAIARLHQLEEDNCVFIQQN
Sbjct: 181 RLCQEYGHAGVELFVYGQEATNPHAPKPLKFPARQTLEASMAIARLHQLEEDNCVFIQQN 240

Query: 241 PAVIDQGVFHNDVIAVGNQNVLFYHEQAFLNTQAKLDEIKRKLDTELYFIEVPTAKVSIN 300
           PAVIDQGVFHNDVIAVGNQNVLFYHEQAFLNTQAKLDEIKRKLDTELYFIEVPTAKVSIN
Sbjct: 241 PAVIDQGVFHNDVIAVGNQNVLFYHEQAFLNTQAKLDEIKRKLDTELYFIEVPTAKVSIN 300

Query: 301 DAVKSYLFNTQIITLPSGEMAIIAPTDCQENPAVYAYLNELLSLNTPIKQVLYFDVKQSM 360
           DAVKSYLFNTQIITLPSGEMAIIAPTDCQENPAVYAYLNELLSLNTPIKQVLYFDVKQSM
Sbjct: 301 DAVKSYLFNTQIITLPSGEMAIIAPTDCQENPAVYAYLNELLSLNTPIKQVLYFDVKQSM 360

Query: 361 QNGGGPACLRLRVAMNEREVAAVNQHTLLTDALFTRLNTWVEKHYRDRLSTEDLADPQLV 420
           QNGGGPACLRLRVAMNEREVAAVNQHTLLTDALFTRLNTWVEKHYRDRLSTEDLADPQLV
Sbjct: 361 QNGGGPACLRLRVAMNEREVAAVNQHTLLTDALFTRLNTWVEKHYRDRLSTEDLADPQLV 420

Query: 421 IESRTALDELTQIMKLGSVYPFQR 444
           IESRTALDELTQIMKLGSVYPFQR
Sbjct: 421 IESRTALDELTQIMKLGSVYPFQR 444


Lambda     K      H
   0.318    0.132    0.387 

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: 783
Number of extensions: 11
Number of successful extensions: 1
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: 444
Length adjustment: 32
Effective length of query: 412
Effective length of database: 412
Effective search space:   169744
Effective search space used:   169744
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 201844 SO2706 (succinylarginine dihydrolase (NCBI ptt file))
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.23900.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   5.5e-225  733.4   0.7   6.2e-225  733.2   0.7    1.0  1  lcl|FitnessBrowser__MR1:201844  SO2706 succinylarginine dihydrol


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:201844  SO2706 succinylarginine dihydrolase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  733.2   0.7  6.2e-225  6.2e-225       2     443 .]       4     443 ..       3     443 .. 0.99

  Alignments for each domain:
  == domain 1  score: 733.2 bits;  conditional E-value: 6.2e-225
                       TIGR03241   2 yevnfdGlvGlthnyaGlsfGnkastsnkksvsnpklaakqGllkmkaladlGfkqgvlapqerpdiaalrklGfsGsd 80 
                                     +e+nfdGlvG+thnyaGlsfGn+as +n   vsnpk+aakqGl+k kaladlG+ qg+lapqerpd+++lr++GfsGsd
  lcl|FitnessBrowser__MR1:201844   4 FEANFDGLVGPTHNYAGLSFGNVASLNNAALVSNPKAAAKQGLQKAKALADLGMIQGMLAPQERPDLNTLRRIGFSGSD 82 
                                     8****************************************************************************** PP

                       TIGR03241  81 eevlekaareapellsavssassmwtanaatvspsadtadgrvhftaanlnnkfhrsieaettervlkaifadekkfav 159
                                     ++vl++aa++ap ll a +sassmwtanaatvspsadt dg++hft+anl  k+hrsie  tt r+l+a+f+d ++f +
  lcl|FitnessBrowser__MR1:201844  83 AQVLQQAAKTAPALLNACCSASSMWTANAATVSPSADTRDGKLHFTPANLVDKLHRSIEPITTGRILTATFNDPHYFYH 161
                                     ******************************************************************************* PP

                       TIGR03241 160 healpavallGdeGaanhtrlgaeydepgvelfvyGraal.erepkpkryparqtleasqavarlhqleeekvvyaqqn 237
                                     h+ lp+++++GdeGaanhtrl++ey+++gvelfvyG++a   ++pkp ++parqtleas a+arlhqlee++ v++qqn
  lcl|FitnessBrowser__MR1:201844 162 HNHLPEHNSFGDEGAANHTRLCQEYGHAGVELFVYGQEATnPHAPKPLKFPARQTLEASMAIARLHQLEEDNCVFIQQN 240
                                     **************************************996789*********************************** PP

                       TIGR03241 238 pdvidqGvfhndviavsnrevlfhhekaflnqsqvldelraklaalgqelvaievpdaevsvedavssylfnsqllske 316
                                     p+vidqGvfhndviav+n++vlf+he+afln+++ lde+++kl++    l  ievp+a+vs++dav+sylfn+q+++  
  lcl|FitnessBrowser__MR1:201844 241 PAVIDQGVFHNDVIAVGNQNVLFYHEQAFLNTQAKLDEIKRKLDTE---LYFIEVPTAKVSINDAVKSYLFNTQIITLP 316
                                     ******************************************9876...9***************************** PP

                       TIGR03241 317 dgkmllvvpeecreneavwayldelvaadgpikevkvfdlresmknGGGpaclrlrvvlndaelaavnpkvllsdalfa 395
                                      g+m ++ p +c+en+av+ayl+el++ ++pik+v  fd+++sm+nGGGpaclrlrv++n+ e+aavn+++ll+dalf+
  lcl|FitnessBrowser__MR1:201844 317 SGEMAIIAPTDCQENPAVYAYLNELLSLNTPIKQVLYFDVKQSMQNGGGPACLRLRVAMNEREVAAVNQHTLLTDALFT 395
                                     ******************************************************************************* PP

                       TIGR03241 396 tlnkwvdrhyrdrlsakdladpqllvesrtaldeltqilnlGsvyefq 443
                                     +ln+wv++hyrdrls++dladpql++esrtaldeltqi++lGsvy+fq
  lcl|FitnessBrowser__MR1:201844 396 RLNTWVEKHYRDRLSTEDLADPQLVIESRTALDELTQIMKLGSVYPFQ 443
                                     ***********************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (443 nodes)
Target sequences:                          1  (444 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: 7.08
//
[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