Alignments for a candidate for speB in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for speB in Pseudomonas putida KT2440

Align agmatinase (EC 3.5.3.11) (characterized)
to candidate PP_4523 PP_4523 putative Agmatinase

Query= BRENDA::W5PHZ9
         (361 letters)



>FitnessBrowser__Putida:PP_4523
          Length = 320

 Score =  407 bits (1045), Expect = e-118
 Identities = 197/316 (62%), Positives = 240/316 (75%)

Query: 43  RQASDGPRNQPPSSEFVARSVGICSMMRLPMQATPEGLDAALVGVPLDIGTSNRPGARFG 102
           R   D   +QP     + R  GI +M+RLP   + +GLDAA +GVPLDIGTS R G RFG
Sbjct: 2   RPTVDKTLHQPLGGNEMPRFGGIATMLRLPHLQSAKGLDAAFIGVPLDIGTSLRSGTRFG 61

Query: 103 PRRIREESVMLRTANPSTGAVPFQFLKVADLGDVNVNLYNLQDSCRLIRADYQKIVAAGC 162
           PR+IR ESVM+R  N +TGA PF  L VAD+GDV +N +NL D+ R+I   Y +IV    
Sbjct: 62  PRQIRAESVMIRPYNMATGAAPFDSLSVADIGDVAINTFNLLDAVRIIEEAYDEIVEHNV 121

Query: 163 VPLTLGGDHTITYPILQAIAEKHGPVGLVHVDAHMDTADKALGEKLYHGTPFRRCVDEGL 222
           +P+TLGGDHTIT PIL+A+ +KHG +GLVH+DAH D  D   GEK+ HGT FRR V+EGL
Sbjct: 122 IPMTLGGDHTITLPILRALHKKHGKIGLVHIDAHADVNDHMFGEKIAHGTTFRRAVEEGL 181

Query: 223 LDCKRVVQIGIRGSSTTLDTYRYSRSQGFRVVLAEDCWLKSLVPLMGEVRQQMGGRPIYI 282
           LDC RVVQIG+R    T D + +SR QGFRVV AE+CW KSL PLM EVR+++GG P+Y+
Sbjct: 182 LDCDRVVQIGLRAQGYTADDFNWSRRQGFRVVQAEECWHKSLEPLMAEVREKVGGGPVYL 241

Query: 283 SFDIDGLDPAYAPGTGTPEIAGLTPSQALEIIRGCQGLNVVGCDLVEVSPPYDPSGNTAL 342
           SFDIDG+DPA+APGTGTPEI GLT  QA+EIIRGC GL+++GCDLVEVSPPYD +GNT+L
Sbjct: 242 SFDIDGIDPAWAPGTGTPEIGGLTTIQAMEIIRGCHGLDLIGCDLVEVSPPYDTTGNTSL 301

Query: 343 VAANLLFEMLCVLPKV 358
           + ANLLFEMLCVLP V
Sbjct: 302 LGANLLFEMLCVLPGV 317


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: 421
Number of extensions: 14
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: 320
Length adjustment: 28
Effective length of query: 333
Effective length of database: 292
Effective search space:    97236
Effective search space used:    97236
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 PP_4523 PP_4523 (putative 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.8395.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-65  207.0   0.0    2.7e-65  206.7   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_4523  PP_4523 putative Agmatinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_4523  PP_4523 putative Agmatinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.7   0.0   2.7e-65   2.7e-65      14     274 ..      40     312 ..      31     313 .. 0.94

  Alignments for each domain:
  == domain 1  score: 206.7 bits;  conditional E-value: 2.7e-65
                           TIGR01230  14 evvivgiPydattsyrpGsrhgpeaireastnLeayseeld.rdlallkvvDagdlplaaGdaremvekieevve 87 
                                         ++  +g+P+d  ts r G+r+gp +ir  s+ +  y+   +   ++ l v+D gd+ + + +  + v  iee  +
  lcl|FitnessBrowser__Putida:PP_4523  40 DAAFIGVPLDIGTSLRSGTRFGPRQIRAESVMIRPYNMATGaAPFDSLSVADIGDVAINTFNLLDAVRIIEEAYD 114
                                         45578********************************9998678******************9************ PP

                           TIGR01230  88 elleegkfvvaiGGeHsitlpvirAvkkkfeklavvqfDAHtDlrdefegeklshacvmrrvlelg....lnvlq 158
                                         e++e++  ++++GG+H+itlp++rA +kk++k+ +v++DAH+D+ d+  gek+ h ++ rr++e g     +v+q
  lcl|FitnessBrowser__Putida:PP_4523 115 EIVEHNVIPMTLGGDHTITLPILRALHKKHGKIGLVHIDAHADVNDHMFGEKIAHGTTFRRAVEEGlldcDRVVQ 189
                                         ****************************************************************99777779*** PP

                           TIGR01230 159 igiRsg..ikeeadlarennikvlk.relede.....iaevlakvldkpvyvtiDiDvlDPafaPGvgtpepgGl 225
                                         ig+R++  + +++++ r+++ +v++  e  ++     +aev  kv + pvy+++DiD++DPa+aPG+gtpe+gGl
  lcl|FitnessBrowser__Putida:PP_4523 190 IGLRAQgyTADDFNWSRRQGFRVVQaEECWHKsleplMAEVREKVGGGPVYLSFDIDGIDPAWAPGTGTPEIGGL 264
                                         ****97446899**********99855555555666699999********************************* PP

                           TIGR01230 226 tskellklfvlaekekkvvGlDvvEvaPvydssevtaltaaklalelll 274
                                         t+ ++++   ++ +   ++G+D+vEv+P yd++  t l+ a+l  e+l 
  lcl|FitnessBrowser__Putida:PP_4523 265 TTIQAME-IIRGCHGLDLIGCDLVEVSPPYDTTGNTSLLGANLLFEMLC 312
                                         *******.89999**********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (275 nodes)
Target sequences:                          1  (320 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: 9.34
//
[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