Alignments for a candidate for ans in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for ans in Herbaspirillum seropedicae SmR1

Align Glutaminase-asparaginase; L-ASNase/L-GLNase; L-asparagine/L-glutamine amidohydrolase; EC 3.5.1.38 (characterized)
to candidate HSERO_RS19635 HSERO_RS19635 L-asparaginase

Query= SwissProt::O68897
         (362 letters)



>FitnessBrowser__HerbieS:HSERO_RS19635
          Length = 353

 Score =  387 bits (995), Expect = e-112
 Identities = 204/358 (56%), Positives = 263/358 (73%), Gaps = 8/358 (2%)

Query: 6   KTFVPGALALLLLFPVAAQAKEVETKTKLANVVILATGGTIAGAGASAANSATYQAAKVG 65
           K F P  + L L+   AAQA+       L NVVILATGGTIAG GA+   +  Y AAKVG
Sbjct: 3   KIFQPFLVLLCLVAAAAAQAQN------LPNVVILATGGTIAGTGATTTTTVGYTAAKVG 56

Query: 66  IEQLIAGVPELSQIANVRGEQVMQIASESINNENLLQLGRRVAELADSKDVDGIVITHGT 125
           ++ LIA VPEL ++ANVRGEQVMQIASE++NN+  L+LG+RV  L    DVDGIVITHGT
Sbjct: 57  VDALIAAVPELKKVANVRGEQVMQIASENMNNDAWLKLGKRVNTLLAQSDVDGIVITHGT 116

Query: 126 DTLEETAYFLNLVEKTDKPIIVVGSMRPGTAMSADGMLNLYNAVAVAGSKDARGKGVLVT 185
           DT+EETAYFL+LV K+ KP+++VG+MRP TA+SADG +NLYNAV +AGSK+A GKGVLVT
Sbjct: 117 DTIEETAYFLDLVVKSKKPVVIVGAMRPSTAISADGPINLYNAVLLAGSKEAIGKGVLVT 176

Query: 186 MNDEIQSGRDVSKMINIKTEAFKSP-WGPLGMVVEGKSYWFRLPAKRHTMDSEFDIKTIK 244
           +ND+I +GR+V+K      + FK+P  G LG +   K Y++R   +++T+D+ FDI  + 
Sbjct: 177 LNDQINAGREVTKTNTSTLDTFKTPELGFLGYIQGSKPYFYRQSTRKNTVDTPFDIMNLD 236

Query: 245 SLPDVEIAYGYGNVSDTAVKALAQAGAKAIIHAGTGNGSVSSKVVPALQELRKQGVQIIR 304
            LP V+I YGY N++  A+ A   AGA+ IIHAG G+GS+++ VVP+L E RK+GV I+R
Sbjct: 237 KLPQVDIVYGYANMNPIALNAFVAAGAQGIIHAGVGDGSLNNTVVPSLTEARKKGVVIVR 296

Query: 305 SSHVNAGGFVLRNAEQPDDKYDWVVAHDLNPQKARILAMVALTKTQDSKELQRMFWEY 362
           SS V   G V RN E  DDK D+VV+  LN QKARIL M+ALTKT D+KE+Q+MFWEY
Sbjct: 297 SSRVGQ-GIVARNGEADDDKLDFVVSDTLNAQKARILLMLALTKTTDTKEIQKMFWEY 353


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: 304
Number of extensions: 7
Number of successful extensions: 3
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: 353
Length adjustment: 29
Effective length of query: 333
Effective length of database: 324
Effective search space:   107892
Effective search space used:   107892
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 HSERO_RS19635 HSERO_RS19635 (L-asparaginase)
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.31825.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   2.8e-147  476.1   5.7   3.2e-147  475.9   5.7    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS19635  HSERO_RS19635 L-asparaginase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS19635  HSERO_RS19635 L-asparaginase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  475.9   5.7  3.2e-147  3.2e-147       9     352 .]      10     353 .]       2     353 .] 0.98

  Alignments for each domain:
  == domain 1  score: 475.9 bits;  conditional E-value: 3.2e-147
                                  TIGR00520   9 laavvlkvsaakaksLPnikilatGGtiagkgqssastaeYkvgklgvedLieavPelkeianiegeq 76 
                                                + + ++ + aa+a++LPn+ ilatGGtiag+g+++++t +Y++ k+gv+ Li avPelk++an++geq
  lcl|FitnessBrowser__HerbieS:HSERO_RS19635  10 VLLCLVAAAAAQAQNLPNVVILATGGTIAGTGATTTTTVGYTAAKVGVDALIAAVPELKKVANVRGEQ 77 
                                                556677788999******************************************************** PP

                                  TIGR00520  77 ivnvgsqdlneevllklakrisealasddvdGivithGtDtleetayfldltvksdkPvvlvGamRpa 144
                                                ++++ s+++n++ +lkl kr+++ la++dvdGivithGtDt+eetayfldl+vks+kPvv+vGamRp+
  lcl|FitnessBrowser__HerbieS:HSERO_RS19635  78 VMQIASENMNNDAWLKLGKRVNTLLAQSDVDGIVITHGTDTIEETAYFLDLVVKSKKPVVIVGAMRPS 145
                                                ******************************************************************** PP

                                  TIGR00520 145 tsvsaDGplnLYnavsvaadeksagrGvlvvlndrilsarevtktnttsldtfkseeqGalGyiandk 212
                                                t++saDGp+nLYnav +a+++++ g+Gvlv+lnd+i  +revtktnt++ldtfk+ e G+lGyi+ +k
  lcl|FitnessBrowser__HerbieS:HSERO_RS19635 146 TAISADGPINLYNAVLLAGSKEAIGKGVLVTLNDQINAGREVTKTNTSTLDTFKTPELGFLGYIQGSK 213
                                                ******************************************************************** PP

                                  TIGR00520 213 ieyerepvkkhtletefdvskldeplPkvdiiYayqnlpeelvkavvdagakGivlagvGnGslsaaa 280
                                                 +++r+ ++k+t++t+fd+ +ld+ lP+vdi+Y+y+n+ +  ++a v aga+Gi+ agvG+Gsl++++
  lcl|FitnessBrowser__HerbieS:HSERO_RS19635 214 PYFYRQSTRKNTVDTPFDIMNLDK-LPQVDIVYGYANMNPIALNAFVAAGAQGIIHAGVGDGSLNNTV 280
                                                ************************.******************************************* PP

                                  TIGR00520 281 lkvleeaakesvvivrssRvadGvvtkdaevddk.ealiasgtLnPqkaRvLLqLaLtktkdlekiqe 347
                                                +  l ea k++vvivrssRv +G+v+++ e dd   +++ s+tLn qkaR+LL+LaLtkt d+++iq+
  lcl|FitnessBrowser__HerbieS:HSERO_RS19635 281 VPSLTEARKKGVVIVRSSRVGQGIVARNGEADDDkLDFVVSDTLNAQKARILLMLALTKTTDTKEIQK 348
                                                *****************************9998779******************************** PP

                                  TIGR00520 348 vfeey 352
                                                +f ey
  lcl|FitnessBrowser__HerbieS:HSERO_RS19635 349 MFWEY 353
                                                **887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (352 nodes)
Target sequences:                          1  (353 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: 6.32
//
[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