Alignments for a candidate for speB in Desulfovibrio vulgaris Hildenborough

GapMind for catabolism of small carbon sources

Alignments for a candidate for speB in Desulfovibrio vulgaris Hildenborough

Align N1-aminopropylagmatine ureohydrolase (EC 3.5.3.24) (characterized)
to candidate 209357 DVU0421 agmatinase, putative

Query= BRENDA::Q5JI38
         (288 letters)



>MicrobesOnline__882:209357
          Length = 290

 Score =  139 bits (351), Expect = 6e-38
 Identities = 95/289 (32%), Positives = 145/289 (50%), Gaps = 18/289 (6%)

Query: 10  LKLEFPLVEPEKARFILLGVPFDGTTSYKAGARFGPTLIRQATLNLESYILDYDLDIAEL 69
           L  E   + PE+ARF ++  PF+ + SY  G   GP  I  A+  LE +      D   +
Sbjct: 10  LASELDDIAPEEARFHVIPAPFEASVSYGGGTGAGPDAILDASDQLELW------DGLSI 63

Query: 70  PIAD---IGDIAVVAGDPRKTADRVRETLEELKKANPKAIPILLGGEHSQTLGAVEALKP 126
           P A            GD     DR+      +  A     P+LLGGEH+ T GA+ AL+ 
Sbjct: 64  PAAQGIHTHPPVDCTGDAEAVLDRISRATRSVLDAG--GTPVLLGGEHTVTYGALAALRE 121

Query: 127 A----SYVVFDAHLDLRNSYEDNPYNHACVARR-ISELGVKEAIFGIRSGTKEEVDFARE 181
                  V FDAH DLR+SYE + ++HA V RR +S+LG+    +G+R+   EEV F RE
Sbjct: 122 RFGRFGVVQFDAHADLRDSYEGSRWSHASVMRRAVSDLGLPLVQYGVRALCTEEVAFRRE 181

Query: 182 RDIPWVHARDYSFDAFV--DLVEALPEPVYLSIDIDVFDLSMVPSTGTPEAGGLRFWEVV 239
             +    A   +        L +  PE VY++ D+D  D S++P+TGTP  GGL +++ +
Sbjct: 182 AGVTHWDAAQLARSGVPARPLPDDFPESVYVTFDVDGLDPSIMPATGTPVPGGLGWYDAL 241

Query: 240 EAIEWLVEKKEIAGFDIMEVAGEKLGDPTALTAAKLLFYSIGAMAKFGR 288
             +E  V  + + GFD++E+A           AA+L++  +G + +  R
Sbjct: 242 RLVERSVSGRRVLGFDVVELAPIAGWHAADFAAARLVYDIMGIIQRMAR 290


Lambda     K      H
   0.319    0.139    0.405 

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: 253
Number of extensions: 15
Number of successful extensions: 5
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: 288
Length of database: 290
Length adjustment: 26
Effective length of query: 262
Effective length of database: 264
Effective search space:    69168
Effective search space used:    69168
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 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate 209357 DVU0421 (agmatinase, putative)
to HMM TIGR01230 (speB: agmatinase (EC 3.5.3.11))

# 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/TIGR01230.hmm
# target sequence database:        /tmp/gapView.22257.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01230  [M=275]
Accession:   TIGR01230
Description: agmatinase: agmatinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
    8.6e-68  214.9   0.0    1.1e-67  214.6   0.0    1.1  1  lcl|MicrobesOnline__882:209357  DVU0421 agmatinase, putative


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:209357  DVU0421 agmatinase, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.6   0.0   1.1e-67   1.1e-67       3     274 ..       9     283 ..       7     284 .. 0.90

  Alignments for each domain:
  == domain 1  score: 214.6 bits;  conditional E-value: 1.1e-67
                       TIGR01230   3 fleseae...yeeAevvivgiPydattsyrpGsrhgpeaireastnLeayseeldrdlallkvvDa.gdlplaaGdare 77 
                                     fl+se +    eeA   +++ P++a++sy  G+  gp+ai++as++Le  +      +  ++ + +   +++ +Gda++
  lcl|MicrobesOnline__882:209357   9 FLASELDdiaPEEARFHVIPAPFEASVSYGGGTGAGPDAILDASDQLELWDGL---SIPAAQGIHThPPVDC-TGDAEA 83 
                                     5666655444699***********************************98853...2333333333034555.9***** PP

                       TIGR01230  78 mvekieevveelleegkfvvaiGGeHsitlpvirAvkkkfeklavvqfDAHtDlrdefegeklshacvmrr.vlelgln 155
                                     ++++i   ++++l++g  +v +GGeH++t++ + A +++f+ + vvqfDAH+Dlrd +eg++ sha+vmrr v +lgl+
  lcl|MicrobesOnline__882:209357  84 VLDRISRATRSVLDAGGTPVLLGGEHTVTYGALAALRERFGRFGVVQFDAHADLRDSYEGSRWSHASVMRRaVSDLGLP 162
                                     *********************************************************************99456999** PP

                       TIGR01230 156 vlqigiRsgikeeadlarennikvlk.relede..iaevlakvldkpvyvtiDiDvlDPafaPGvgtpepgGltskell 231
                                      +q+g+R+ + ee  + re ++   +  +l+ +   a+ l+ ++ + vyvt+D+D+lDP+ +P +gtp+pgGl+++++l
  lcl|MicrobesOnline__882:209357 163 LVQYGVRALCTEEVAFRREAGVTHWDaAQLARSgvPARPLPDDFPESVYVTFDVDGLDPSIMPATGTPVPGGLGWYDAL 241
                                     *********************97777677776666789999************************************** PP

                       TIGR01230 232 klfvlaekekkvvGlDvvEvaPvydssevtaltaaklalelll 274
                                     +l ++  +  +v G+DvvE+aP +   + ++++aa+l++++++
  lcl|MicrobesOnline__882:209357 242 RLVERSVSGRRVLGFDVVELAP-IAGWHAADFAAARLVYDIMG 283
                                     **********************.788999***********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (275 nodes)
Target sequences:                          1  (290 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: 6.00
//
[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