Alignments for a candidate for speB in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for speB in Pseudomonas fluorescens GW456-L13

Align Agmatinase; Agmatine ureohydrolase; AUH; EC 3.5.3.11 (characterized)
to candidate PfGW456L13_2989 Agmatinase (EC 3.5.3.11)

Query= SwissProt::Q7X3P1
         (306 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2989
          Length = 319

 Score =  322 bits (826), Expect = 6e-93
 Identities = 158/280 (56%), Positives = 204/280 (72%), Gaps = 6/280 (2%)

Query: 31  YSSD---ADWVITGVPFDMATSGRAGTRHGPGAIRQISTNLAWEGHRWPWHFDMRERLKV 87
           YS D    D  ++GVPFD ATS R G R GP  IR  S  +AWE H WPW FD  + L V
Sbjct: 36  YSRDLRGVDVAVSGVPFDTATSNRPGARFGPRGIRAASAGIAWERH-WPWTFDPFDHLAV 94

Query: 88  VDCGDLVFNFGDAQDMSDKLQAHTEKLLAAGKRCLTFGGDHFVTLPLLRAHAKHFGKMAL 147
           +D GD  F++G  Q   + ++AH E +L AG   LTFGGDHF+T PLL+AHA+  G ++L
Sbjct: 95  IDYGDCDFDYGSPQSTPEMIEAHAEHILNAGTAMLTFGGDHFITYPLLKAHARKHGALSL 154

Query: 148 VHFDAHTDTYAN--GSKFDHGTMFYHAPNEGLIDPQHSVQIGIRTEHDTNNGFTVLDAAQ 205
           +HFDAH+DT+ +  G + DHGTMF+HA  EGL+DP  SVQIG+RT +D + GF VLDA Q
Sbjct: 155 IHFDAHSDTWPDEEGKRIDHGTMFWHAAREGLVDPSRSVQIGLRTTNDDHQGFEVLDARQ 214

Query: 206 VNDRGVDDLVAQIKEIVGSLPVYLTFDIDCLDPAFAPGTGTPVVGGLTTDKALKMLRALQ 265
           V+ RG + +V  I+  VG  PVYLTFDIDCLDPAFAPGTGTPV GGL+T +AL++L  L+
Sbjct: 215 VHRRGCEAIVEAIRARVGDNPVYLTFDIDCLDPAFAPGTGTPVCGGLSTVQALEILGGLR 274

Query: 266 PLNIVGMDLVEVSPAYDQSDITALAGATIALDMLYLQAAK 305
            +N+VGMD+VEV+PAYD ++IT+LA AT+A++ML L AA+
Sbjct: 275 GINLVGMDVVEVAPAYDSAEITSLAAATLAMEMLCLYAAR 314


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: 341
Number of extensions: 16
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: 319
Length adjustment: 27
Effective length of query: 279
Effective length of database: 292
Effective search space:    81468
Effective search space used:    81468
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 PfGW456L13_2989 (Agmatinase (EC 3.5.3.11))
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.1804736.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
    1.2e-78  250.5   0.0    1.4e-78  250.3   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2989  Agmatinase (EC 3.5.3.11)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2989  Agmatinase (EC 3.5.3.11)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  250.3   0.0   1.4e-78   1.4e-78      13     274 ..      43     309 ..      30     310 .. 0.93

  Alignments for each domain:
  == domain 1  score: 250.3 bits;  conditional E-value: 1.4e-78
                                               TIGR01230  13 AevvivgiPydattsyrpGsrhgpeaireastnLeayseeldrdlal...lkvvD 64 
                                                              +v + g+P+d++ts rpG+r+gp  ir as +++++ +  ++ ++    l v+D
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2989  43 VDVAVSGVPFDTATSNRPGARFGPRGIRAASAGIAWERH-WPWTFDPfdhLAVID 96 
                                                             58899******************************9865.5665554444***** PP

                                               TIGR01230  65 agdlplaaGdaremvekieevveelleegkfvvaiGGeHsitlpvirAvkkkfek 119
                                                              gd ++ +G+++   e+ie+++e++l++g  ++++GG+H+it+p+++A+++k++ 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2989  97 YGDCDFDYGSPQSTPEMIEAHAEHILNAGTAMLTFGGDHFITYPLLKAHARKHGA 151
                                                             ******************************************************* PP

                                               TIGR01230 120 lavvqfDAHtDlr.....defegeklshacvmrrvlelglnvlqigiRsgikeea 169
                                                             l +++fDAH D+         +++++++ ++ ++++++  +++qig+R+  ++ +
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2989 152 LSLIHFDAHSDTWpdeegKRIDHGTMFWHAAREGLVDPS-RSVQIGLRTTNDDHQ 205
                                                             ************976666667888888888999999999.9************** PP

                                               TIGR01230 170 dlarennikvlkreledeiaevlakvldkpvyvtiDiDvlDPafaPGvgtpepgG 224
                                                             ++ + ++ +v +r  e   +   a+v d+pvy+t+DiD+lDPafaPG+gtp+ gG
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2989 206 GFEVLDARQVHRRGCEAIVEAIRARVGDNPVYLTFDIDCLDPAFAPGTGTPVCGG 260
                                                             ******************************************************* PP

                                               TIGR01230 225 ltskellklfvlaekekkvvGlDvvEvaPvydssevtaltaaklalelll 274
                                                             l++ ++l+  + +    ++vG+DvvEvaP+yds+e+t l+aa+la+e+l 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2989 261 LSTVQALE-ILGGLRGINLVGMDVVEVAPAYDSAEITSLAAATLAMEMLC 309
                                                             ********.67788999*******************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (275 nodes)
Target sequences:                          1  (319 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 22.29
//
[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