Alignments for a candidate for speB in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for speB in Dinoroseobacter shibae DFL-12

Align Agmatinase; Agmatine ureohydrolase; AUH; EC 3.5.3.11 (characterized)
to candidate 3608333 Dshi_1735 putative agmatinase (RefSeq)

Query= SwissProt::Q7X3P1
         (306 letters)



>FitnessBrowser__Dino:3608333
          Length = 324

 Score =  251 bits (640), Expect = 2e-71
 Identities = 135/288 (46%), Positives = 185/288 (64%), Gaps = 5/288 (1%)

Query: 18  AFGFLRFPLNFQPYSSDADWVITGVPFDMATSGRAGTRHGPGAIRQISTNLAWEGHRWPW 77
           A  FLR    +    S  D  ++GVPFD++ + R G R GP AIR+ S+   ++   + W
Sbjct: 31  ALSFLR--RRYTKELSGVDVAVSGVPFDLSVTNRPGCRLGPRAIREASSLQPFDPP-YGW 87

Query: 78  HFDMRERLKVVDCGDLVFNFGDAQDMSDKLQAHTEKLLAAGKRCLTFGGDHFVTLPLLRA 137
            FD      VVD GDL F++G A      L+AH   +LAAG   LT GGDH+++ P+LRA
Sbjct: 88  GFDPLSEFTVVDYGDLAFDYGRAAGFPAALEAHIRTILAAGAAPLTMGGDHYISYPILRA 147

Query: 138 HAKHFGKMALVHFDAHTDTYANGSK--FDHGTMFYHAPNEGLIDPQHSVQIGIRTEHDTN 195
            A+  G ++L+ FDAH+DT+ +  +   DHGTMFY A  +GLIDP  SVQ+GIRT +DT+
Sbjct: 148 LAEVHGPLSLLQFDAHSDTWPDEDRDRLDHGTMFYKAVKDGLIDPARSVQVGIRTTNDTD 207

Query: 196 NGFTVLDAAQVNDRGVDDLVAQIKEIVGSLPVYLTFDIDCLDPAFAPGTGTPVVGGLTTD 255
            GF V+DA +V++ G   + A+++ I+G    YLTFDIDCLDP  APGTGTPV GGL+  
Sbjct: 208 LGFHVIDAREVHEAGAAAVAAKVRGILGDHKTYLTFDIDCLDPGTAPGTGTPVWGGLSAG 267

Query: 256 KALKMLRALQPLNIVGMDLVEVSPAYDQSDITALAGATIALDMLYLQA 303
           +A  +LR L  + +VG D+VEVSP YD S  TA+AGA +  ++L L A
Sbjct: 268 QAAILLRDLAGITVVGGDVVEVSPPYDPSGATAVAGAHVMTEILCLWA 315


Lambda     K      H
   0.321    0.138    0.426 

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: 330
Number of extensions: 12
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: 306
Length of database: 324
Length adjustment: 27
Effective length of query: 279
Effective length of database: 297
Effective search space:    82863
Effective search space used:    82863
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 (21.9 bits)
S2: 48 (23.1 bits)

Align candidate 3608333 Dshi_1735 (putative agmatinase (RefSeq))
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.6071.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    1.4e-64  204.4   0.0    1.6e-64  204.1   0.0    1.0  1  lcl|FitnessBrowser__Dino:3608333  Dshi_1735 putative agmatinase (R


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3608333  Dshi_1735 putative agmatinase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.1   0.0   1.6e-64   1.6e-64      12     274 ..      45     312 ..      34     313 .. 0.95

  Alignments for each domain:
  == domain 1  score: 204.1 bits;  conditional E-value: 1.6e-64
                         TIGR01230  12 eAevvivgiPydattsyrpGsrhgpeaireastnLeayseeldrdlal...lkvvDagdlplaaGdaremvekieev 85 
                                         +v + g+P+d ++  rpG+r gp aireas  L+ +++ +++ ++      vvD gdl + +G a      +e++
  lcl|FitnessBrowser__Dino:3608333  45 GVDVAVSGVPFDLSVTNRPGCRLGPRAIREAS-SLQPFDPPYGWGFDPlseFTVVDYGDLAFDYGRAAGFPAALEAH 120
                                       568999*************************9.59********8877655599************************ PP

                         TIGR01230  86 veelleegkfvvaiGGeHsitlpvirAvkkkfeklavvqfDAHtDlr.....defegeklshacvmrrvlelglnvl 157
                                       ++ +l++g  ++++GG+H i++p++rA ++ +++l ++qfDAH D+      d  +++++++ +v+ +++++  +++
  lcl|FitnessBrowser__Dino:3608333 121 IRTILAAGAAPLTMGGDHYISYPILRALAEVHGPLSLLQFDAHSDTWpdedrDRLDHGTMFYKAVKDGLIDPA-RSV 196
                                       *********************************************977666699******************9.9** PP

                         TIGR01230 158 qigiRsgikeeadlarennikvlkreledeiaevlakvldkpvyvtiDiDvlDPafaPGvgtpepgGltskellklf 234
                                       q+giR+  + + ++ + ++ +v +   + + a+v  ++ d++ y+t+DiD+lDP+ aPG+gtp+ gGl+  ++   +
  lcl|FitnessBrowser__Dino:3608333 197 QVGIRTTNDTDLGFHVIDAREVHEAGAAAVAAKVRGILGDHKTYLTFDIDCLDPGTAPGTGTPVWGGLSAGQAAI-L 272
                                       *********************************************************************998865.8 PP

                         TIGR01230 235 vlaekekkvvGlDvvEvaPvydssevtaltaaklalelll 274
                                       ++      vvG DvvEv+P yd s  ta++ a ++ e+l 
  lcl|FitnessBrowser__Dino:3608333 273 LRDLAGITVVGGDVVEVSPPYDPSGATAVAGAHVMTEILC 312
                                       99999******************************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (275 nodes)
Target sequences:                          1  (324 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: 00:00:00.00
# Mc/sec: 9.85
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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