Alignments for a candidate for speB in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for speB in Burkholderia phytofirmans PsJN

Align agmatinase (EC 3.5.3.11) (characterized)
to candidate BPHYT_RS31515 BPHYT_RS31515 agmatinase

Query= BRENDA::W5PHZ9
         (361 letters)



>FitnessBrowser__BFirm:BPHYT_RS31515
          Length = 324

 Score =  288 bits (738), Expect = 1e-82
 Identities = 149/308 (48%), Positives = 203/308 (65%), Gaps = 6/308 (1%)

Query: 53  PPSSEFVARSVGICSMMRLP-MQATPEGL---DAALVGVPLDIGTSNRPGARFGPRRIRE 108
           P +   + R  G+ ++MRLP M+ T   +   D  L+GVP D GT+NRPGAR GPR++R+
Sbjct: 8   PVTGTMMPRYAGVATLMRLPHMELTNNSIKDVDIGLIGVPWDGGTTNRPGARHGPRQVRD 67

Query: 109 ESVMLRTANPSTGAVPFQFLKVADLGDVNVNLYNLQDSCRLIRADYQKIVAAGCVPLTLG 168
            S M+R  N S+   PF     ADLGD  VN  +L DS   I   Y ++   G  PL++G
Sbjct: 68  ISTMVRNVNRSSNINPFGLCNCADLGDAPVNPVDLIDSLNRIAGFYDEVCKLGIAPLSVG 127

Query: 169 GDHTITYPILQAIAEKHGPVGLVHVDAHMDTADKALGEKLY-HGTPFRRCVDEGLLDCKR 227
           GDH +T PI++ +A K  P+G+VH DAH DT ++  G+ +Y HGTPFRR ++EGLLD KR
Sbjct: 128 GDHLVTLPIMRGLA-KDRPLGMVHFDAHTDTWNRYFGDNIYTHGTPFRRAIEEGLLDPKR 186

Query: 228 VVQIGIRGSSTTLDTYRYSRSQGFRVVLAEDCWLKSLVPLMGEVRQQMGGRPIYISFDID 287
            VQIGIRG+        +   +G RV+  ++     +  ++ E R+ +G  P Y++FD+D
Sbjct: 187 TVQIGIRGALYNDSENDWGEREGIRVIDIDEFHAMGIDAVIQEARRVVGDGPTYVTFDVD 246

Query: 288 GLDPAYAPGTGTPEIAGLTPSQALEIIRGCQGLNVVGCDLVEVSPPYDPSGNTALVAANL 347
            LDP +APGTGTPEI GLT  +A  +IRG +GLN+VG D+VEVSPP+DPSGNTALV A L
Sbjct: 247 ALDPVFAPGTGTPEIGGLTTLEAQHMIRGLRGLNLVGGDVVEVSPPFDPSGNTALVGATL 306

Query: 348 LFEMLCVL 355
           +FE+LCVL
Sbjct: 307 MFEILCVL 314


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: 409
Number of extensions: 22
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: 361
Length of database: 324
Length adjustment: 29
Effective length of query: 332
Effective length of database: 295
Effective search space:    97940
Effective search space used:    97940
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 BPHYT_RS31515 BPHYT_RS31515 (agmatinase)
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.16654.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
    8.5e-60  188.7   0.0    1.1e-59  188.3   0.0    1.1  1  lcl|FitnessBrowser__BFirm:BPHYT_RS31515  BPHYT_RS31515 agmatinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS31515  BPHYT_RS31515 agmatinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.3   0.0   1.1e-59   1.1e-59       7     274 ..      33     312 ..      27     313 .. 0.90

  Alignments for each domain:
  == domain 1  score: 188.3 bits;  conditional E-value: 1.1e-59
                                TIGR01230   7 eaeyeeAevvivgiPydattsyrpGsrhgpeaireastnLeayseeld.rdlallkvvDagdlplaaGda 75 
                                              + + ++ ++ ++g+P+d  t  rpG+rhgp ++r++st + + +   +   ++l + +D+gd p+   d 
  lcl|FitnessBrowser__BFirm:BPHYT_RS31515  33 NNSIKDVDIGLIGVPWDGGTTNRPGARHGPRQVRDISTMVRNVNRSSNiNPFGLCNCADLGDAPVNPVDL 102
                                              45578899999***************************9999888888455999***********99**9 PP

                                TIGR01230  76 remvekieevveelleegkfvvaiGGeHsitlpvirAvkkkfeklavvqfDAHtDlrdefegek.lshac 144
                                               +++++i    +e+ + g  ++++GG+H++tlp++r  +k  ++l +v+fDAHtD+   + g++ ++h +
  lcl|FitnessBrowser__BFirm:BPHYT_RS31515 103 IDSLNRIAGFYDEVCKLGIAPLSVGGDHLVTLPIMRGLAKD-RPLGMVHFDAHTDTWNRYFGDNiYTHGT 171
                                              *************************************9875.89*************9888765268*** PP

                                TIGR01230 145 vmrrvlelg....lnvlqigiRsgi..keeadlarennikvlk.relede.....iaevlakvldkpvyv 202
                                              + rr++e g    ++++qigiR  +  + e+d+ ++++i+v++  e++       i+e+   v d p yv
  lcl|FitnessBrowser__BFirm:BPHYT_RS31515 172 PFRRAIEEGlldpKRTVQIGIRGALynDSENDWGEREGIRVIDiDEFHAMgidavIQEARRVVGDGPTYV 241
                                              *******9988889********986337799**********98545544454444888888999****** PP

                                TIGR01230 203 tiDiDvlDPafaPGvgtpepgGltskellklfvlaekekkvvGlDvvEvaPvydssevtaltaaklalel 272
                                              t+D+D+lDP faPG+gtpe+gGlt+ e+ + + ++    ++vG DvvEv+P +d s  tal  a+l+ e+
  lcl|FitnessBrowser__BFirm:BPHYT_RS31515 242 TFDVDALDPVFAPGTGTPEIGGLTTLEAQH-MIRGLRGLNLVGGDVVEVSPPFDPSGNTALVGATLMFEI 310
                                              ****************************99.8999**********************************9 PP

                                TIGR01230 273 ll 274
                                              l 
  lcl|FitnessBrowser__BFirm:BPHYT_RS31515 311 LC 312
                                              85 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 8.22
//
[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