Alignments for a candidate for ans in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for ans in Pseudomonas simiae WCS417

Align Glutaminase-asparaginase; L-ASNase/L-GLNase; L-asparagine/L-glutamine amidohydrolase; EC 3.5.1.38 (characterized)
to candidate GFF3596 PS417_18410 glutaminase

Query= SwissProt::O68897
         (362 letters)



>FitnessBrowser__WCS417:GFF3596
          Length = 362

 Score =  680 bits (1755), Expect = 0.0
 Identities = 352/362 (97%), Positives = 355/362 (98%)

Query: 1   MKSALKTFVPGALALLLLFPVAAQAKEVETKTKLANVVILATGGTIAGAGASAANSATYQ 60
           MKSALK FVPGALALLLLFPVAAQAKEVE+KTKL+NVVILATGGTIAGAGASAANSATYQ
Sbjct: 1   MKSALKNFVPGALALLLLFPVAAQAKEVESKTKLSNVVILATGGTIAGAGASAANSATYQ 60

Query: 61  AAKVGIEQLIAGVPELSQIANVRGEQVMQIASESINNENLLQLGRRVAELADSKDVDGIV 120
           AAKVGIEQLIAGVPELSQIANVRGEQVMQIASESINNENLLQLGRRVAELADSKDVDGIV
Sbjct: 61  AAKVGIEQLIAGVPELSQIANVRGEQVMQIASESINNENLLQLGRRVAELADSKDVDGIV 120

Query: 121 ITHGTDTLEETAYFLNLVEKTDKPIIVVGSMRPGTAMSADGMLNLYNAVAVAGSKDARGK 180
           ITHGTDTLEETAYFLNLVEKTDKPI+VVGSMRPGTAMSADGMLNLYNAVAVAGSKDARGK
Sbjct: 121 ITHGTDTLEETAYFLNLVEKTDKPIVVVGSMRPGTAMSADGMLNLYNAVAVAGSKDARGK 180

Query: 181 GVLVTMNDEIQSGRDVSKMINIKTEAFKSPWGPLGMVVEGKSYWFRLPAKRHTMDSEFDI 240
           GVLVTMNDEIQSGRDVSKMINIKTEAFKSPWGPLGMVVEGKSYWFRLPAKRHTMDSEFDI
Sbjct: 181 GVLVTMNDEIQSGRDVSKMINIKTEAFKSPWGPLGMVVEGKSYWFRLPAKRHTMDSEFDI 240

Query: 241 KTIKSLPDVEIAYGYGNVSDTAVKALAQAGAKAIIHAGTGNGSVSSKVVPALQELRKQGV 300
           K IKSLPDVEIAYGYGNVSDTA KALAQAGAKAIIHAGTGNGSVSSKVVPAL ELRKQGV
Sbjct: 241 KNIKSLPDVEIAYGYGNVSDTAYKALAQAGAKAIIHAGTGNGSVSSKVVPALVELRKQGV 300

Query: 301 QIIRSSHVNAGGFVLRNAEQPDDKYDWVVAHDLNPQKARILAMVALTKTQDSKELQRMFW 360
           QIIRSSHVNAGG VLRNAEQPDDKYDWV A DLNPQKARILAMVALTKTQDSKELQRMFW
Sbjct: 301 QIIRSSHVNAGGMVLRNAEQPDDKYDWVAALDLNPQKARILAMVALTKTQDSKELQRMFW 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: 458
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 GFF3596 PS417_18410 (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.14732.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   2.5e-124  400.6   2.3     3e-124  400.4   2.3    1.0  1  lcl|FitnessBrowser__WCS417:GFF3596  PS417_18410 glutaminase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF3596  PS417_18410 glutaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  400.4   2.3    3e-124    3e-124      17     352 .]      27     362 .]      14     362 .] 0.96

  Alignments for each domain:
  == domain 1  score: 400.4 bits;  conditional E-value: 3e-124
                           TIGR00520  17 saakaksLPnikilatGGtiagkgqssastaeYkvgklgvedLieavPelkeianiegeqivnvgsqdlneevll 91 
                                         +++ +++L n+ ilatGGtiag+g+s a+ a Y++ k+g+e+Li  vPel++ian++geq++++ s+++n+e ll
  lcl|FitnessBrowser__WCS417:GFF3596  27 EVESKTKLSNVVILATGGTIAGAGASAANSATYQAAKVGIEQLIAGVPELSQIANVRGEQVMQIASESINNENLL 101
                                         4556899******************************************************************** PP

                           TIGR00520  92 klakrisealasddvdGivithGtDtleetayfldltvksdkPvvlvGamRpatsvsaDGplnLYnavsvaadek 166
                                         +l +r+ e  +s+dvdGivithGtDtleetayfl+l+ k+dkP+v+vG+mRp t++saDG lnLYnav+va++++
  lcl|FitnessBrowser__WCS417:GFF3596 102 QLGRRVAELADSKDVDGIVITHGTDTLEETAYFLNLVEKTDKPIVVVGSMRPGTAMSADGMLNLYNAVAVAGSKD 176
                                         *************************************************************************** PP

                           TIGR00520 167 sagrGvlvvlndrilsarevtktnttsldtfkseeqGalGyiandkieyerepvkkhtletefdvskldeplPkv 241
                                         ++g+Gvlv++nd+i s+r+v k+   ++++fks   G lG ++++k ++ r p+k+ht+++efd+++ ++ lP+v
  lcl|FitnessBrowser__WCS417:GFF3596 177 ARGKGVLVTMNDEIQSGRDVSKMINIKTEAFKSP-WGPLGMVVEGKSYWFRLPAKRHTMDSEFDIKNIKS-LPDV 249
                                         *********************************9.***********************************.**** PP

                           TIGR00520 242 diiYayqnlpeelvkavvdagakGivlagvGnGslsaaalkvleeaakesvvivrssRvadG.vvtkd.aevddk 314
                                         +i Y+y n++++  ka+++agak i+ ag+GnGs+s +++ +l e+ k++v i+rss v+ G +v ++ +++ddk
  lcl|FitnessBrowser__WCS417:GFF3596 250 EIAYGYGNVSDTAYKALAQAGAKAIIHAGTGNGSVSSKVVPALVELRKQGVQIIRSSHVNAGgMVLRNaEQPDDK 324
                                         **********************************************************99763666551568889 PP

                           TIGR00520 315 ealiasgtLnPqkaRvLLqLaLtktkdlekiqevfeey 352
                                         ++ +a+  LnPqkaR+L ++aLtkt+d +++q++f ey
  lcl|FitnessBrowser__WCS417:GFF3596 325 YDWVAALDLNPQKARILAMVALTKTQDSKELQRMFWEY 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: 9.53
//
[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