Alignments for a candidate for aguB in Desulfovibrio vulgaris Miyazaki F

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.6477.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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.62
//
[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