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

GapMind for catabolism of small carbon sources

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

Align Glutaminase-asparaginase; L-ASNase/L-GLNase; L-asparagine/L-glutamine amidohydrolase; EC 3.5.1.38 (characterized)
to candidate AO353_20805 AO353_20805 glutaminase

Query= SwissProt::O68897
         (362 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_20805
          Length = 362

 Score =  659 bits (1700), Expect = 0.0
 Identities = 333/362 (91%), Positives = 346/362 (95%)

Query: 1   MKSALKTFVPGALALLLLFPVAAQAKEVETKTKLANVVILATGGTIAGAGASAANSATYQ 60
           MKSA  TF+PGALALLLL P A QAKEVET+ KLANVV+LATGGTIAGAGAS+ANSATYQ
Sbjct: 1   MKSAFNTFIPGALALLLLLPTALQAKEVETRQKLANVVVLATGGTIAGAGASSANSATYQ 60

Query: 61  AAKVGIEQLIAGVPELSQIANVRGEQVMQIASESINNENLLQLGRRVAELADSKDVDGIV 120
           AAKVGIEQLIAG+PELSQ+ANVRGEQVMQIASESI NENLLQLGRRVAELADSKDVDGIV
Sbjct: 61  AAKVGIEQLIAGIPELSQLANVRGEQVMQIASESITNENLLQLGRRVAELADSKDVDGIV 120

Query: 121 ITHGTDTLEETAYFLNLVEKTDKPIIVVGSMRPGTAMSADGMLNLYNAVAVAGSKDARGK 180
           ITHGTDTLEETAYFLNLVEKTDKPII+VGSMRPGTAMSADGMLNLYNAVAVAGSKDARGK
Sbjct: 121 ITHGTDTLEETAYFLNLVEKTDKPIIIVGSMRPGTAMSADGMLNLYNAVAVAGSKDARGK 180

Query: 181 GVLVTMNDEIQSGRDVSKMINIKTEAFKSPWGPLGMVVEGKSYWFRLPAKRHTMDSEFDI 240
           GVLVTMNDEIQSGRDVSKM+N+KTEAFKSPWGPLGMV+EGKSYWFRLPAKRHTMDSEFDI
Sbjct: 181 GVLVTMNDEIQSGRDVSKMVNLKTEAFKSPWGPLGMVIEGKSYWFRLPAKRHTMDSEFDI 240

Query: 241 KTIKSLPDVEIAYGYGNVSDTAVKALAQAGAKAIIHAGTGNGSVSSKVVPALQELRKQGV 300
           K IKSLPDVEIAY YGNV  TA KALAQ+GAKAIIHAGTGNGSVSS++VP LQELRK GV
Sbjct: 241 KNIKSLPDVEIAYSYGNVDGTAYKALAQSGAKAIIHAGTGNGSVSSRLVPTLQELRKDGV 300

Query: 301 QIIRSSHVNAGGFVLRNAEQPDDKYDWVVAHDLNPQKARILAMVALTKTQDSKELQRMFW 360
           QIIRSSHVNAGGFVLRNAEQPDDKYDWVVAHDLNPQKARIL MVALTKT DSKELQRMFW
Sbjct: 301 QIIRSSHVNAGGFVLRNAEQPDDKYDWVVAHDLNPQKARILTMVALTKTSDSKELQRMFW 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: 446
Number of extensions: 6
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 AO353_20805 AO353_20805 (glutaminase)
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.20852.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   3.4e-122  393.6   0.7   4.1e-122  393.4   0.7    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_20805  AO353_20805 glutaminase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_20805  AO353_20805 glutaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  393.4   0.7  4.1e-122  4.1e-122      16     352 .]      26     362 .]      14     362 .] 0.96

  Alignments for each domain:
  == domain 1  score: 393.4 bits;  conditional E-value: 4.1e-122
                                     TIGR00520  16 vsaakaksLPnikilatGGtiagkgqssastaeYkvgklgvedLieavPelkeianiegeqivnv 80 
                                                    +++ +++L n+ +latGGtiag+g+ssa+ a Y++ k+g+e+Li  +Pel+++an++geq++++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_20805  26 KEVETRQKLANVVVLATGGTIAGAGASSANSATYQAAKVGIEQLIAGIPELSQLANVRGEQVMQI 90 
                                                   34556899********************************************************* PP

                                     TIGR00520  81 gsqdlneevllklakrisealasddvdGivithGtDtleetayfldltvksdkPvvlvGamRpat 145
                                                    s+++ +e ll+l +r+ e  +s+dvdGivithGtDtleetayfl+l+ k+dkP+++vG+mRp t
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_20805  91 ASESITNENLLQLGRRVAELADSKDVDGIVITHGTDTLEETAYFLNLVEKTDKPIIIVGSMRPGT 155
                                                   ***************************************************************** PP

                                     TIGR00520 146 svsaDGplnLYnavsvaadeksagrGvlvvlndrilsarevtktnttsldtfkseeqGalGyian 210
                                                   ++saDG lnLYnav+va++++++g+Gvlv++nd+i s+r+v k+   ++++fks   G lG + +
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_20805 156 AMSADGMLNLYNAVAVAGSKDARGKGVLVTMNDEIQSGRDVSKMVNLKTEAFKSP-WGPLGMVIE 219
                                                   ******************************************************9.********* PP

                                     TIGR00520 211 dkieyerepvkkhtletefdvskldeplPkvdiiYayqnlpeelvkavvdagakGivlagvGnGs 275
                                                   +k ++ r p+k+ht+++efd+++ ++ lP+v+i Y+y n+  +  ka++++gak i+ ag+GnGs
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_20805 220 GKSYWFRLPAKRHTMDSEFDIKNIKS-LPDVEIAYSYGNVDGTAYKALAQSGAKAIIHAGTGNGS 283
                                                   **************************.************************************** PP

                                     TIGR00520 276 lsaaalkvleeaakesvvivrssRvadG.vvt.kdaevddkealiasgtLnPqkaRvLLqLaLtk 338
                                                   +s   + +l+e+ k++v i+rss v+ G  v  +++++ddk++ + +  LnPqkaR+L ++aLtk
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_20805 284 VSSRLVPTLQELRKDGVQIIRSSHVNAGgFVLrNAEQPDDKYDWVVAHDLNPQKARILTMVALTK 348
                                                   *************************9873444155678999************************ PP

                                     TIGR00520 339 tkdlekiqevfeey 352
                                                   t d +++q++f ey
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_20805 349 TSDSKELQRMFWEY 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.52
//
[ok]

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

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Protein sequences (fasta format)
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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