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

GapMind for catabolism of small carbon sources

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

Align Glutaminase-asparaginase; L-ASNase/L-GLNase; L-asparagine/L-glutamine amidohydrolase; EC 3.5.1.38 (characterized)
to candidate PfGW456L13_3914 L-asparaginase (EC 3.5.1.1)

Query= SwissProt::O68897
         (362 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3914
          Length = 362

 Score =  659 bits (1701), Expect = 0.0
 Identities = 340/362 (93%), Positives = 348/362 (96%)

Query: 1   MKSALKTFVPGALALLLLFPVAAQAKEVETKTKLANVVILATGGTIAGAGASAANSATYQ 60
           M SALKTFVPGALALLLL P A QAKE ET+ KLANVVILATGGTIAGAGASAANSATYQ
Sbjct: 1   MTSALKTFVPGALALLLLLPTALQAKEAETQQKLANVVILATGGTIAGAGASAANSATYQ 60

Query: 61  AAKVGIEQLIAGVPELSQIANVRGEQVMQIASESINNENLLQLGRRVAELADSKDVDGIV 120
           AAKVGIEQLIAGVPELSQ+ANVRGEQVMQIASESI NENLLQLGRRVAELADSKDVDGIV
Sbjct: 61  AAKVGIEQLIAGVPELSQLANVRGEQVMQIASESITNENLLQLGRRVAELADSKDVDGIV 120

Query: 121 ITHGTDTLEETAYFLNLVEKTDKPIIVVGSMRPGTAMSADGMLNLYNAVAVAGSKDARGK 180
           ITHGTDTLEETAYFLNLVEKT+KPIIVVGSMRPGTAMSADGMLNLYNAVAVA SKDARGK
Sbjct: 121 ITHGTDTLEETAYFLNLVEKTEKPIIVVGSMRPGTAMSADGMLNLYNAVAVASSKDARGK 180

Query: 181 GVLVTMNDEIQSGRDVSKMINIKTEAFKSPWGPLGMVVEGKSYWFRLPAKRHTMDSEFDI 240
           GVLVTMNDEIQSGRDVSKMINIKTEAFKS WGPLGMVVEGKSYW+RLPAKRHTMDSEFDI
Sbjct: 181 GVLVTMNDEIQSGRDVSKMINIKTEAFKSAWGPLGMVVEGKSYWYRLPAKRHTMDSEFDI 240

Query: 241 KTIKSLPDVEIAYGYGNVSDTAVKALAQAGAKAIIHAGTGNGSVSSKVVPALQELRKQGV 300
           KTIKSLPDVEIAY YGNVSDTA KALAQ+GAKAIIHAGTGNGSVSS+VVPALQ LRK GV
Sbjct: 241 KTIKSLPDVEIAYSYGNVSDTAYKALAQSGAKAIIHAGTGNGSVSSRVVPALQALRKDGV 300

Query: 301 QIIRSSHVNAGGFVLRNAEQPDDKYDWVVAHDLNPQKARILAMVALTKTQDSKELQRMFW 360
           QIIRSSHVNAGGFVLRNAEQPDDKYDWVVA+DLNPQKAR+LAMVALTKT DSKELQRMFW
Sbjct: 301 QIIRSSHVNAGGFVLRNAEQPDDKYDWVVANDLNPQKARVLAMVALTKTNDSKELQRMFW 360

Query: 361 EY 362
           EY
Sbjct: 361 EY 362


Lambda     K      H
   0.315    0.130    0.361 

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: 449
Number of extensions: 5
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: 362
Length of database: 362
Length adjustment: 29
Effective length of query: 333
Effective length of database: 333
Effective search space:   110889
Effective search space used:   110889
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 (21.5 bits)
S2: 49 (23.5 bits)

Align candidate PfGW456L13_3914 (L-asparaginase (EC 3.5.1.1))
to HMM TIGR00520 (L-asparaginase, type II (EC 3.5.1.1))

# 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/TIGR00520.hmm
# target sequence database:        /tmp/gapView.30156.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00520  [M=352]
Accession:   TIGR00520
Description: asnASE_II: L-asparaginase, type II
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   4.1e-124  399.9   2.6   4.8e-124  399.7   2.6    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3914  L-asparaginase (EC 3.5.1.1)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3914  L-asparaginase (EC 3.5.1.1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  399.7   2.6  4.8e-124  4.8e-124      15     352 .]      25     362 .]      13     362 .] 0.96

  Alignments for each domain:
  == domain 1  score: 399.7 bits;  conditional E-value: 4.8e-124
                                               TIGR00520  15 kvsaakaksLPnikilatGGtiagkgqssastaeYkvgklgvedLieavPelkei 69 
                                                               +a+ +++L n+ ilatGGtiag+g+s a+ a Y++ k+g+e+Li  vPel+++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3914  25 AKEAETQQKLANVVILATGGTIAGAGASAANSATYQAAKVGIEQLIAGVPELSQL 79 
                                                             344566999********************************************** PP

                                               TIGR00520  70 aniegeqivnvgsqdlneevllklakrisealasddvdGivithGtDtleetayf 124
                                                             an++geq++++ s+++ +e ll+l +r+ e  +s+dvdGivithGtDtleetayf
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3914  80 ANVRGEQVMQIASESITNENLLQLGRRVAELADSKDVDGIVITHGTDTLEETAYF 134
                                                             ******************************************************* PP

                                               TIGR00520 125 ldltvksdkPvvlvGamRpatsvsaDGplnLYnavsvaadeksagrGvlvvlndr 179
                                                             l+l+ k++kP+++vG+mRp t++saDG lnLYnav+va++++++g+Gvlv++nd+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3914 135 LNLVEKTEKPIIVVGSMRPGTAMSADGMLNLYNAVAVASSKDARGKGVLVTMNDE 189
                                                             ******************************************************* PP

                                               TIGR00520 180 ilsarevtktnttsldtfkseeqGalGyiandkieyerepvkkhtletefdvskl 234
                                                             i s+r+v k+   ++++fks   G lG ++++k +++r p+k+ht+++efd++  
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3914 190 IQSGRDVSKMINIKTEAFKSA-WGPLGMVVEGKSYWYRLPAKRHTMDSEFDIKTI 243
                                                             ********************9.********************************* PP

                                               TIGR00520 235 deplPkvdiiYayqnlpeelvkavvdagakGivlagvGnGslsaaalkvleeaak 289
                                                             ++ lP+v+i Y+y n++++  ka++++gak i+ ag+GnGs+s  ++ +l+ + k
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3914 244 KS-LPDVEIAYSYGNVSDTAYKALAQSGAKAIIHAGTGNGSVSSRVVPALQALRK 297
                                                             **.**************************************************** PP

                                               TIGR00520 290 esvvivrssRvadG.vvt.kdaevddkealiasgtLnPqkaRvLLqLaLtktkdl 342
                                                             ++v i+rss v+ G  v  +++++ddk++ + ++ LnPqkaRvL ++aLtkt+d 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3914 298 DGVQIIRSSHVNAGgFVLrNAEQPDDKYDWVVANDLNPQKARVLAMVALTKTNDS 352
                                                             ***********9873444155678999**************************** PP

                                               TIGR00520 343 ekiqevfeey 352
                                                             +++q++f ey
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3914 353 KELQRMFWEY 362
                                                             *******887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (352 nodes)
Target sequences:                          1  (362 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: 10.03
//
[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