Alignments for a candidate for speB in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for speB in Pseudomonas simiae WCS417

Align agmatinase (EC 3.5.3.11) (characterized)
to candidate GFF3941 PS417_20180 agmatinase

Query= BRENDA::W5PHZ9
         (361 letters)



>FitnessBrowser__WCS417:GFF3941
          Length = 316

 Score =  405 bits (1040), Expect = e-117
 Identities = 196/308 (63%), Positives = 236/308 (76%)

Query: 51  NQPPSSEFVARSVGICSMMRLPMQATPEGLDAALVGVPLDIGTSNRPGARFGPRRIREES 110
           +QP     + R  GI +MMRLP   T +GLDAA +GVPLDIGTS R G RFGPR IR ES
Sbjct: 6   HQPLGGNEMPRFAGIATMMRLPHLQTAKGLDAAFIGVPLDIGTSLRAGTRFGPREIRAES 65

Query: 111 VMLRTANPSTGAVPFQFLKVADLGDVNVNLYNLQDSCRLIRADYQKIVAAGCVPLTLGGD 170
           VM+R  N +TGA PF  L VAD+GDV +N +NL D+ R+I   Y +I+    +PLTLGGD
Sbjct: 66  VMIRPYNMATGAAPFDSLSVADIGDVAINTFNLLDAVRIIEEAYDEILEHDVIPLTLGGD 125

Query: 171 HTITYPILQAIAEKHGPVGLVHVDAHMDTADKALGEKLYHGTPFRRCVDEGLLDCKRVVQ 230
           HTIT PIL+AI +KHG VGLVH+DAH D  D   GEK+ HGT FRR V+EGLLDC RVVQ
Sbjct: 126 HTITLPILRAIHKKHGKVGLVHIDAHADVNDHMFGEKIAHGTTFRRAVEEGLLDCDRVVQ 185

Query: 231 IGIRGSSTTLDTYRYSRSQGFRVVLAEDCWLKSLVPLMGEVRQQMGGRPIYISFDIDGLD 290
           IG+R    T + + +SR QGFRVV AE+CW  SL PLM EVR+++ G P+Y+SFDIDG+D
Sbjct: 186 IGLRAQGYTAEDFNWSRKQGFRVVQAEECWHHSLAPLMAEVREKVDGGPVYLSFDIDGID 245

Query: 291 PAYAPGTGTPEIAGLTPSQALEIIRGCQGLNVVGCDLVEVSPPYDPSGNTALVAANLLFE 350
           PA+APGTGTPEI GLT  QA+EIIRGCQGL+++GCDLVEVSPPYD +GNT+L+ ANLL+E
Sbjct: 246 PAWAPGTGTPEIGGLTTIQAIEIIRGCQGLDLIGCDLVEVSPPYDTTGNTSLLGANLLYE 305

Query: 351 MLCVLPKV 358
           MLCVLP V
Sbjct: 306 MLCVLPGV 313


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: 418
Number of extensions: 13
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: 316
Length adjustment: 28
Effective length of query: 333
Effective length of database: 288
Effective search space:    95904
Effective search space used:    95904
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 GFF3941 PS417_20180 (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.26047.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
      2e-66  210.4   0.0    2.4e-66  210.1   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF3941  PS417_20180 agmatinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF3941  PS417_20180 agmatinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.1   0.0   2.4e-66   2.4e-66      14     274 ..      36     308 ..      25     309 .. 0.93

  Alignments for each domain:
  == domain 1  score: 210.1 bits;  conditional E-value: 2.4e-66
                           TIGR01230  14 evvivgiPydattsyrpGsrhgpeaireastnLeayseeld.rdlallkvvDagdlplaaGdaremvekieevve 87 
                                         ++  +g+P+d  ts r+G+r+gp  ir  s+ +  y+   +   ++ l v+D gd+ + + +  + v  iee  +
  lcl|FitnessBrowser__WCS417:GFF3941  36 DAAFIGVPLDIGTSLRAGTRFGPREIRAESVMIRPYNMATGaAPFDSLSVADIGDVAINTFNLLDAVRIIEEAYD 110
                                         45568********************************9998678******************9************ PP

                           TIGR01230  88 elleegkfvvaiGGeHsitlpvirAvkkkfeklavvqfDAHtDlrdefegeklshacvmrrvlelg....lnvlq 158
                                         e+le+   ++++GG+H+itlp++rA++kk++k+ +v++DAH+D+ d+  gek+ h ++ rr++e g     +v+q
  lcl|FitnessBrowser__WCS417:GFF3941 111 EILEHDVIPLTLGGDHTITLPILRAIHKKHGKVGLVHIDAHADVNDHMFGEKIAHGTTFRRAVEEGlldcDRVVQ 185
                                         ****************************************************************99777779*** PP

                           TIGR01230 159 igiRsg..ikeeadlarennikvlk.relede.....iaevlakvldkpvyvtiDiDvlDPafaPGvgtpepgGl 225
                                         ig+R++  + e++++ r+++ +v++  e  ++     +aev  kv + pvy+++DiD++DPa+aPG+gtpe+gGl
  lcl|FitnessBrowser__WCS417:GFF3941 186 IGLRAQgyTAEDFNWSRKQGFRVVQaEECWHHslaplMAEVREKVDGGPVYLSFDIDGIDPAWAPGTGTPEIGGL 260
                                         ****974478************9985554444556669999999999**************************** PP

                           TIGR01230 226 tskellklfvlaekekkvvGlDvvEvaPvydssevtaltaaklalelll 274
                                         t+ ++++   ++ +   ++G+D+vEv+P yd++  t l+ a+l +e+l 
  lcl|FitnessBrowser__WCS417:GFF3941 261 TTIQAIE-IIRGCQGLDLIGCDLVEVSPPYDTTGNTSLLGANLLYEMLC 308
                                         *******.899************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (275 nodes)
Target sequences:                          1  (316 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 9.80
//
[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