GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aguB in Desulfovibrio vulgaris Miyazaki F

Align N-carbamoylputrescine amidase; EC 3.5.1.53 (characterized)
to candidate 8499888 DvMF_0653 N-carbamoylputrescine amidase (RefSeq)

Query= SwissProt::Q9XGI9
         (300 letters)



>FitnessBrowser__Miya:8499888
          Length = 313

 Score =  356 bits (914), Expect = e-103
 Identities = 173/288 (60%), Positives = 211/288 (73%), Gaps = 4/288 (1%)

Query: 8   VTVAALQFACTDDVSTNVATAERLVRAAHQKGANIILIQELFEGYYFCQAQKEEFFHRAK 67
           V VAA Q ACTD+ S N+     LVR A   GA+I+L QELF G YFC+ +  E F  A+
Sbjct: 4   VIVAATQMACTDNESRNIDRVCELVREAAAMGAHIVLPQELFSGPYFCKDELPEHFALAR 63

Query: 68  PYPGHPTIVRMQNLAKELGVVIPVSFFEEANNAHYNSVAIIDADGTDLGLYRKSHIPDGP 127
           P    P + RM  LA ELGVVIPVSFFE +N  +YNS+A+IDADG  +GLYRKSHIP GP
Sbjct: 64  PLDESPAVRRMSALAAELGVVIPVSFFERSNQVYYNSLAMIDADGRVMGLYRKSHIPQGP 123

Query: 128 GYQEKYYFNPGDTGFKVFQTKYAKIGVAICWDQWFPEAARAMALQGAEVLFYPTAIGSEP 187
           GY+EK+YF+PGDTGF+V++T+Y  +GV +CWDQWFPE AR+MAL GA+VL YPTAIGSEP
Sbjct: 124 GYEEKFYFSPGDTGFRVWRTRYGTVGVGVCWDQWFPECARSMALLGADVLLYPTAIGSEP 183

Query: 188 QDDGLDSRDHWRRVMQGHAGANVVPLVASNRIGKEIIETEHGNSEITFYGYSFIAGPTGE 247
            +   DS  HW R MQGHA AN++PLVASNR+G+E  +       +TFYG SFIAGP GE
Sbjct: 184 AEPACDSSGHWTRTMQGHAAANMMPLVASNRVGEEFGK----GFSMTFYGSSFIAGPQGE 239

Query: 248 LVAAAGDKEEAVLVAQFDLDKIKSKRHGWGVYRDRRPDLYKVLLTLDG 295
           +V  AG  EE VL A FD + I+++R GWG++RDRRPDLY  LLT DG
Sbjct: 240 IVQQAGRSEECVLTAAFDFEAIRAERAGWGLFRDRRPDLYHPLLTFDG 287


Lambda     K      H
   0.319    0.137    0.414 

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: 342
Number of extensions: 12
Number of successful extensions: 2
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: 300
Length of database: 313
Length adjustment: 27
Effective length of query: 273
Effective length of database: 286
Effective search space:    78078
Effective search space used:    78078
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate 8499888 DvMF_0653 (N-carbamoylputrescine amidase (RefSeq))
to HMM TIGR03381 (aguB: N-carbamoylputrescine amidase (EC 3.5.1.53))

# 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/TIGR03381.hmm
# target sequence database:        /tmp/gapView.14952.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03381  [M=279]
Accession:   TIGR03381
Description: agmatine_aguB: N-carbamoylputrescine amidase
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-142  459.0   0.0   3.2e-142  458.8   0.0    1.0  1  lcl|FitnessBrowser__Miya:8499888  DvMF_0653 N-carbamoylputrescine 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8499888  DvMF_0653 N-carbamoylputrescine amidase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  458.8   0.0  3.2e-142  3.2e-142       1     278 [.       4     281 ..       4     282 .. 0.99

  Alignments for each domain:
  == domain 1  score: 458.8 bits;  conditional E-value: 3.2e-142
                         TIGR03381   1 vkvaavqlalsedveeniekaeklvreaaakGaqiillpelfeapyfckeqeeeyfelakpveehplikrlqklake 77 
                                       v vaa+q+a++++ ++ni+++ +lvreaaa Ga+i+l++elf++pyfck++  e+f+la+p++e+p+++r+++la+e
  lcl|FitnessBrowser__Miya:8499888   4 VIVAATQMACTDNESRNIDRVCELVREAAAMGAHIVLPQELFSGPYFCKDELPEHFALARPLDESPAVRRMSALAAE 80 
                                       569************************************************************************** PP

                         TIGR03381  78 levvlpvsffekagnalynslavidadGevlgvyrkshiPdgpgyeekfyfkpGdtGfkvwdtryakiGvgicWdqW 154
                                       l+vv+pvsffe++++++ynsla+idadG+v+g+yrkshiP+gpgyeekfyf+pGdtGf+vw+try+ +Gvg+cWdqW
  lcl|FitnessBrowser__Miya:8499888  81 LGVVIPVSFFERSNQVYYNSLAMIDADGRVMGLYRKSHIPQGPGYEEKFYFSPGDTGFRVWRTRYGTVGVGVCWDQW 157
                                       ***************************************************************************** PP

                         TIGR03381 155 fpeaaralalkGaevllyPtaiGsePadaeldskehWqramqGhaaanvvpvvaanrigkeveaeleltfyGssfia 231
                                       fpe+ar++al Ga+vllyPtaiGsePa+++ ds+ hW+r+mqGhaaan++p+va+nr+g+e  ++ ++tfyGssfia
  lcl|FitnessBrowser__Miya:8499888 158 FPECARSMALLGADVLLYPTAIGSEPAEPACDSSGHWTRTMQGHAAANMMPLVASNRVGEEFGKGFSMTFYGSSFIA 234
                                       ***************************************************************************** PP

                         TIGR03381 232 detGelvaeadrseeavlvaefdldeiakeraawGlfrdrrpelyek 278
                                         +Ge+v++a+rsee vl+a fd+++i++era wGlfrdrrp+ly+ 
  lcl|FitnessBrowser__Miya:8499888 235 GPQGEIVQQAGRSEECVLTAAFDFEAIRAERAGWGLFRDRRPDLYHP 281
                                       *********************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (279 nodes)
Target sequences:                          1  (313 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 9.68
//
[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:

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:

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:

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:

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