GapMind for catabolism of small carbon sources

 

Alignments for a candidate for speB in Paraburkholderia bryophila 376MFSha3.1

Align agmatinase (EC 3.5.3.11) (characterized)
to candidate H281DRAFT_00178 H281DRAFT_00178 agmatinase

Query= BRENDA::W5PHZ9
         (361 letters)



>FitnessBrowser__Burk376:H281DRAFT_00178
          Length = 329

 Score =  406 bits (1043), Expect = e-118
 Identities = 200/311 (64%), Positives = 235/311 (75%)

Query: 48  GPRNQPPSSEFVARSVGICSMMRLPMQATPEGLDAALVGVPLDIGTSNRPGARFGPRRIR 107
           G R QP S   + RS GI +MMRLP   + EG DA  VGVP D+GTSNR GARFGPR+IR
Sbjct: 12  GERPQPLSGNAMPRSGGIATMMRLPNVGSAEGFDACFVGVPFDLGTSNRTGARFGPRQIR 71

Query: 108 EESVMLRTANPSTGAVPFQFLKVADLGDVNVNLYNLQDSCRLIRADYQKIVAAGCVPLTL 167
            ESV+LR  N +T A PF  L+VADLGDV +N YNL DS   I   Y +I+   C P+TL
Sbjct: 72  SESVLLRPYNMATRAAPFDSLRVADLGDVAINPYNLHDSIARIETAYDEILQHDCKPVTL 131

Query: 168 GGDHTITYPILQAIAEKHGPVGLVHVDAHMDTADKALGEKLYHGTPFRRCVDEGLLDCKR 227
           GGDHTI  PIL+AI  KHG VGL+HVDAH D  D  +GEK+ HGTPFRR V+EGLLDC+R
Sbjct: 132 GGDHTIALPILRAIHRKHGKVGLIHVDAHADVNDTMMGEKIAHGTPFRRAVEEGLLDCER 191

Query: 228 VVQIGIRGSSTTLDTYRYSRSQGFRVVLAEDCWLKSLVPLMGEVRQQMGGRPIYISFDID 287
           VVQIG+RG+    + + + R QGF VV AE CW +SL PLM  VR++MG  P+YI+FDID
Sbjct: 192 VVQIGLRGTGYAAEDFDWCRDQGFDVVQAEACWNQSLAPLMARVRERMGDGPVYITFDID 251

Query: 288 GLDPAYAPGTGTPEIAGLTPSQALEIIRGCQGLNVVGCDLVEVSPPYDPSGNTALVAANL 347
           G+DPA+APGTGTPEIAGLT  QALEIIRG +GLN+VGCDLVEV+PPYDP G TAL+AANL
Sbjct: 252 GIDPAFAPGTGTPEIAGLTVPQALEIIRGARGLNIVGCDLVEVAPPYDPFGTTALLAANL 311

Query: 348 LFEMLCVLPKV 358
            FE+LCVLP V
Sbjct: 312 AFELLCVLPGV 322


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: 427
Number of extensions: 15
Number of successful extensions: 1
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: 329
Length adjustment: 29
Effective length of query: 332
Effective length of database: 300
Effective search space:    99600
Effective search space used:    99600
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 H281DRAFT_00178 H281DRAFT_00178 (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.11665.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
    2.2e-68  216.9   0.0    2.6e-68  216.6   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_00178  H281DRAFT_00178 agmatinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_00178  H281DRAFT_00178 agmatinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.6   0.0   2.6e-68   2.6e-68      12     274 ..      43     317 ..      32     318 .. 0.93

  Alignments for each domain:
  == domain 1  score: 216.6 bits;  conditional E-value: 2.6e-68
                                    TIGR01230  12 eAevvivgiPydattsyrpGsrhgpeaireastnLeayseeld.rdlallkvvDagdlplaaGdar 76 
                                                    ++  vg+P+d  ts r G+r+gp +ir  s+ L  y+       ++ l+v+D+gd+ +   + +
  lcl|FitnessBrowser__Burk376:H281DRAFT_00178  43 GFDACFVGVPFDLGTSNRTGARFGPRQIRSESVLLRPYNMATRaAPFDSLRVADLGDVAINPYNLH 108
                                                  5578899*******************************98877588**************99999* PP

                                    TIGR01230  77 emvekieevveelleegkfvvaiGGeHsitlpvirAvkkkfeklavvqfDAHtDlrdefegeklsh 142
                                                  +++ +ie   +e+l++  ++v++GG+H+i+lp++rA+++k++k+ ++++DAH+D+ d   gek+ h
  lcl|FitnessBrowser__Burk376:H281DRAFT_00178 109 DSIARIETAYDEILQHDCKPVTLGGDHTIALPILRAIHRKHGKVGLIHVDAHADVNDTMMGEKIAH 174
                                                  ****************************************************************** PP

                                    TIGR01230 143 acvmrrvlelg....lnvlqigiRsg..ikeeadlarennikvlkrelede......iaevlakvl 196
                                                   ++ rr++e g     +v+qig+R      e++d+ r+++ +v++ e   +      +a+v  ++ 
  lcl|FitnessBrowser__Burk376:H281DRAFT_00178 175 GTPFRRAVEEGlldcERVVQIGLRGTgyAAEDFDWCRDQGFDVVQAEACWNqslaplMARVRERMG 240
                                                  *********99877789*******753378*************9966554446666688999999* PP

                                    TIGR01230 197 dkpvyvtiDiDvlDPafaPGvgtpepgGltskellklfvlaekekkvvGlDvvEvaPvydssevta 262
                                                  d pvy+t+DiD++DPafaPG+gtpe++Glt  ++l+   ++    ++vG+D+vEvaP yd    ta
  lcl|FitnessBrowser__Burk376:H281DRAFT_00178 241 DGPVYITFDIDGIDPAFAPGTGTPEIAGLTVPQALE-IIRGARGLNIVGCDLVEVAPPYDPFGTTA 305
                                                  ************************************.889999*********************** PP

                                    TIGR01230 263 ltaaklalelll 274
                                                  l+aa+la ell 
  lcl|FitnessBrowser__Burk376:H281DRAFT_00178 306 LLAANLAFELLC 317
                                                  *********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (275 nodes)
Target sequences:                          1  (329 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: 00:00:00.01
# Mc/sec: 8.29
//
[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:

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:

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:

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:

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