Alignments for a candidate for speB in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for speB in Cupriavidus basilensis 4G11

Align agmatinase (EC 3.5.3.11) (characterized)
to candidate RR42_RS02455 RR42_RS02455 agmatinase

Query= BRENDA::W5PHZ9
         (361 letters)



>FitnessBrowser__Cup4G11:RR42_RS02455
          Length = 328

 Score =  391 bits (1005), Expect = e-113
 Identities = 191/307 (62%), Positives = 229/307 (74%)

Query: 52  QPPSSEFVARSVGICSMMRLPMQATPEGLDAALVGVPLDIGTSNRPGARFGPRRIREESV 111
           QP S   + R  GI +MMRLP  A+  GLDA  VGVP D+GTSNR GAR GPR+IR ESV
Sbjct: 17  QPMSGNAMPRFGGIATMMRLPAAASTAGLDACFVGVPFDLGTSNRNGARLGPRQIRAESV 76

Query: 112 MLRTANPSTGAVPFQFLKVADLGDVNVNLYNLQDSCRLIRADYQKIVAAGCVPLTLGGDH 171
           +LR  N +T A PF  L+VAD+GDV  N YNL D+   I A Y+ I+A GC P+ LGGDH
Sbjct: 77  LLRPYNMATRAAPFDSLRVADIGDVATNPYNLHDAIARIEAAYRDIIATGCRPIGLGGDH 136

Query: 172 TITYPILQAIAEKHGPVGLVHVDAHMDTADKALGEKLYHGTPFRRCVDEGLLDCKRVVQI 231
           T+T PIL+A+  +HG +GL+HVDAH D  D   GEK+ HGTPFRR V+EGLLDC RVVQI
Sbjct: 137 TVTLPILRAMHARHGRLGLIHVDAHADVNDTMFGEKIAHGTPFRRAVEEGLLDCGRVVQI 196

Query: 232 GIRGSSTTLDTYRYSRSQGFRVVLAEDCWLKSLVPLMGEVRQQMGGRPIYISFDIDGLDP 291
           G+RG+    + + + R QGFRV+ AE CW +SL PLM E+  ++ G P+YISFDIDG+DP
Sbjct: 197 GLRGTGYAAEDFDWCRQQGFRVITAEACWYRSLAPLMEEIGMRLQGGPVYISFDIDGIDP 256

Query: 292 AYAPGTGTPEIAGLTPSQALEIIRGCQGLNVVGCDLVEVSPPYDPSGNTALVAANLLFEM 351
           AYAPGTGTPEI GLT  QALEIIRG +GL++VG DLVEVSPPYDP G TAL+ ANL FE+
Sbjct: 257 AYAPGTGTPEIGGLTVPQALEIIRGARGLDIVGADLVEVSPPYDPFGTTALLGANLAFEL 316

Query: 352 LCVLPKV 358
           LCVLP V
Sbjct: 317 LCVLPGV 323


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: 449
Number of extensions: 18
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: 328
Length adjustment: 29
Effective length of query: 332
Effective length of database: 299
Effective search space:    99268
Effective search space used:    99268
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 RR42_RS02455 RR42_RS02455 (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.9897.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.5e-63  201.0   0.0    1.9e-63  200.7   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS02455  RR42_RS02455 agmatinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS02455  RR42_RS02455 agmatinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.7   0.0   1.9e-63   1.9e-63      10     274 ..      42     318 ..      33     319 .. 0.91

  Alignments for each domain:
  == domain 1  score: 200.7 bits;  conditional E-value: 1.9e-63
                                 TIGR01230  10 yeeAevvivgiPydattsyrpGsrhgpeaireastnLeayseeld.rdlallkvvDagdlplaaGdare 77 
                                               ++  ++  vg+P+d  ts r+G+r gp +ir  s+ L  y+       ++ l+v+D gd+ +   + ++
  lcl|FitnessBrowser__Cup4G11:RR42_RS02455  42 TAGLDACFVGVPFDLGTSNRNGARLGPRQIRAESVLLRPYNMATRaAPFDSLRVADIGDVATNPYNLHD 110
                                               455688899*******************************98877588**************99999** PP

                                 TIGR01230  78 mvekieevveelleegkfvvaiGGeHsitlpvirAvkkkfeklavvqfDAHtDlrdefegeklshacvm 146
                                                + +ie+  +++++ g +++++GG+H++tlp++rA++ +++ l ++++DAH+D+ d   gek+ h ++ 
  lcl|FitnessBrowser__Cup4G11:RR42_RS02455 111 AIARIEAAYRDIIATGCRPIGLGGDHTVTLPILRAMHARHGRLGLIHVDAHADVNDTMFGEKIAHGTPF 179
                                               ********************************************************************* PP

                                 TIGR01230 147 rrvlelg....lnvlqigiRsg..ikeeadlarennikvl.....k.reledeiaevlakvldkpvyvt 203
                                               rr++e g     +v+qig+R      e++d+ r+++ +v+     + r+l+  ++e  +++ + pvy++
  lcl|FitnessBrowser__Cup4G11:RR42_RS02455 180 RRAVEEGlldcGRVVQIGLRGTgyAAEDFDWCRQQGFRVItaeacWyRSLAPLMEEIGMRLQGGPVYIS 248
                                               *****99766669*******753378**********9997222223345555588888899999***** PP

                                 TIGR01230 204 iDiDvlDPafaPGvgtpepgGltskellklfvlaekekkvvGlDvvEvaPvydssevtaltaaklalel 272
                                               +DiD++DPa+aPG+gtpe+gGlt  ++l+   ++     +vG+D+vEv+P yd    tal+ a+la el
  lcl|FitnessBrowser__Cup4G11:RR42_RS02455 249 FDIDGIDPAYAPGTGTPEIGGLTVPQALE-IIRGARGLDIVGADLVEVSPPYDPFGTTALLGANLAFEL 316
                                               *****************************.8899999*******************************9 PP

                                 TIGR01230 273 ll 274
                                               l 
  lcl|FitnessBrowser__Cup4G11:RR42_RS02455 317 LC 318
                                               96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (275 nodes)
Target sequences:                          1  (328 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: 10.09
//
[ok]

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

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Steps (tab-delimited)
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Protein sequences (fasta format)
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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