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 (EC 3.5.3.11) (characterized)
to candidate PfGW456L13_2689 Agmatinase (EC 3.5.3.11)

Query= BRENDA::W5PHZ9
         (361 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2689
          Length = 333

 Score =  170 bits (431), Expect = 4e-47
 Identities = 108/305 (35%), Positives = 167/305 (54%), Gaps = 23/305 (7%)

Query: 63  VGICSMMRLPMQATPEGLDA--ALVGVPLDIGTSNRPGARFGPRRIREESVMLRTANPST 120
           VG C+  + P+    + LDA  A++GVP D+GT  R GARFGPR IRE S +    +   
Sbjct: 16  VGHCTFGKSPVCTDWDALDADVAVLGVPNDMGTQWRSGARFGPRGIREASTLFSFGH--A 73

Query: 121 GAVPFQF---------LKVADLGDVNVNLYNLQDSCRLIRADYQKIVAAGCVPLTLGGDH 171
           GA   +          +++ D+GD ++   ++  S +      +KI+ AG +P+ LGGDH
Sbjct: 74  GAYDHEDDVMYLTASDVRMVDVGDADIVHTDMATSNKNTEYAVRKILDAGVMPVVLGGDH 133

Query: 172 TITYPILQAIAEKHGPVGLVHVDAHMDTADKALGEKLYHGTPFRRCVDEGLLDCKRVVQI 231
           ++  P+++A  E  GP+ ++H DAH+D  D+  G +  HG P RR  +   +    + Q+
Sbjct: 134 SVHAPVIKAF-EGRGPIHIIHFDAHLDFVDERHGVRYGHGNPLRRASEMNHI--VGMTQM 190

Query: 232 GIRG-SSTTLDTYRYSRSQGFRVVLAEDCWLKSLVPLMGEVRQQMGGRPIYISFDIDGLD 290
           GIR  SS+  D Y  +   G +++   D     +  ++  + Q +     YI+ DIDG D
Sbjct: 191 GIRNVSSSNRDDYEAAHEAGSKILSVRDVRRLGVEGVLALIPQNIN---YYITIDIDGFD 247

Query: 291 PAYAPGTGTPEIAGLTPSQALEIIRGCQGL---NVVGCDLVEVSPPYDPSGNTALVAANL 347
           P+ APGTGTP   G    + LEII+        N+VG DLVEV+P YDP+G T+++AA L
Sbjct: 248 PSIAPGTGTPSHGGFLYYEVLEIIQALAKRSKGNIVGMDLVEVAPVYDPTGMTSILAAQL 307

Query: 348 LFEML 352
           L   +
Sbjct: 308 LLNSI 312


Lambda     K      H
   0.321    0.139    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: 292
Number of extensions: 13
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: 361
Length of database: 333
Length adjustment: 29
Effective length of query: 332
Effective length of database: 304
Effective search space:   100928
Effective search space used:   100928
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: 49 (23.5 bits)

Align candidate PfGW456L13_2689 (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.13877.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
    2.1e-59  187.4   0.1    2.5e-59  187.1   0.1    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2689  Agmatinase (EC 3.5.3.11)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2689  Agmatinase (EC 3.5.3.11)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.1   0.1   2.5e-59   2.5e-59       8     273 ..      30     312 ..      23     314 .. 0.85

  Alignments for each domain:
  == domain 1  score: 187.1 bits;  conditional E-value: 2.5e-59
                                               TIGR01230   8 aeyeeAevvivgiPydattsyrpGsrhgpeaireastnLeayse.eldrdlal.. 59 
                                                              ++ +A+v ++g+P d+ t +r G+r+gp  ireast     +   +d++ +   
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2689  30 WDALDADVAVLGVPNDMGTQWRSGARFGPRGIREASTLFSFGHAgAYDHEDDVmy 84 
                                                             56779*******************************9876544314443333233 PP

                                               TIGR01230  60 .....lkvvDagdlplaaGdaremvekieevveelleegkfvvaiGGeHsitlpv 109
                                                                  +++vD+gd +++  d   + ++ e  v+++l++g ++v++GG+Hs+  pv
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2689  85 ltasdVRMVDVGDADIVHTDMATSNKNTEYAVRKILDAGVMPVVLGGDHSVHAPV 139
                                                             44566***************99999999999************************ PP

                                               TIGR01230 110 irAvkkkfeklavvqfDAHtDlrdefegeklshacvmrrvlelg..lnvlqigiR 162
                                                             i+A + + +++ +++fDAH D  de +g ++ h  + rr+ e++    ++q+giR
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2689 140 IKAFEGR-GPIHIIHFDAHLDFVDERHGVRYGHGNPLRRASEMNhiVGMTQMGIR 193
                                                             ***9865.89*********************************94445789**** PP

                                               TIGR01230 163 ...sgikeeadlarennikvlk.reledeiaevlakvldkpv..yvtiDiDvlDP 211
                                                                s  +++ + a+e + k+l+ r++     e +  ++ +++  y+tiDiD++DP
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2689 194 nvsSSNRDDYEAAHEAGSKILSvRDVRRLGVEGVLALIPQNInyYITIDIDGFDP 248
                                                             554456788999*********999**998666666666555555*********** PP

                                               TIGR01230 212 afaPGvgtpepgGltskellk.lfv.laekekkvvGlDvvEvaPvydssevtalt 264
                                                             + aPG+gtp  gG+  +e+l+ +    ++++ ++vG+D+vEvaPvyd + +t ++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2689 249 SIAPGTGTPSHGGFLYYEVLEiIQAlAKRSKGNIVGMDLVEVAPVYDPTGMTSIL 303
                                                             *********************543314567889********************** PP

                                               TIGR01230 265 aaklalell 273
                                                             aa+l l+ +
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2689 304 AAQLLLNSI 312
                                                             ***998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (275 nodes)
Target sequences:                          1  (333 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: 10.88
//
[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