GapMind for catabolism of small carbon sources

 

Aligments for a candidate for sdaB in Pseudomonas fluorescens GW456-L13

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate PfGW456L13_1089 L-serine dehydratase (EC 4.3.1.17)

Query= reanno::pseudo3_N2E3:AO353_15500
         (458 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1089 L-serine
           dehydratase (EC 4.3.1.17)
          Length = 458

 Score =  718 bits (1854), Expect = 0.0
 Identities = 358/458 (78%), Positives = 399/458 (87%)

Query: 1   MAISVFDLFKVGIGPSSSHTVGPMRAAATFAQALFDQGLLEQTRRVEVRLYGSLSATGVG 60
           MAISVFDLFK+GIGPSSSHTVGPMRAAA F Q L ++GLLEQ RRVEV+L+GSLSATG+G
Sbjct: 1   MAISVFDLFKIGIGPSSSHTVGPMRAAALFVQGLRERGLLEQVRRVEVQLFGSLSATGIG 60

Query: 61  HATDRACVMGLMGEWPDSIDPSCIGPRIQQLRESGELLLAGRRSIAFDWQRDLLLLDESL 120
           H +D A +MGLMGEWPD+IDPS IG  I  LRE+  LLL GR  + F W RD+ L+DE+L
Sbjct: 61  HGSDNAVIMGLMGEWPDAIDPSQIGICIANLRETDTLLLDGRLPVPFIWGRDMRLIDENL 120

Query: 121 PYHPNAMSLTAFGESGQLWEQTYYSVGGGFIVEAAEAESGVPASSDVVLPYEFSSAVELL 180
           P+HPNAM+L   G+ G+L   TYYSVGGGF+V+ A+A SGV      VLPY+FSSA ELL
Sbjct: 121 PFHPNAMTLIVEGDDGELHRDTYYSVGGGFVVDEAQASSGVVDLDSTVLPYDFSSAAELL 180

Query: 181 SLCNQHGLRVSELMMANERAWRSDAEIRSGLLHIWSVMRECVEQGLRHEGILPGGLDVPR 240
            LC +H LRV+ELMMANER WRS+ EIRSGL+ +W  M++CVEQGL+HEGILPGGL+V R
Sbjct: 181 ELCKKHNLRVAELMMANERVWRSEDEIRSGLMKLWRAMQDCVEQGLKHEGILPGGLNVRR 240

Query: 241 RAAKLHRSLLEIGKPNVISSTLSAMEWVNLFALAVNEENAAGGRMVTAPTNGAAGIIPAV 300
           RAAKLHRSL E+ KPNVI STLSAMEWVNLFALAVNEENAAGGRMVTAPTNGAAGIIPAV
Sbjct: 241 RAAKLHRSLQELNKPNVIGSTLSAMEWVNLFALAVNEENAAGGRMVTAPTNGAAGIIPAV 300

Query: 301 LHYYMKFNPDASDDDVVAFFLAAASVGILCKKNASISGAEVGCQGEVGSACAMAAAGLAD 360
           LHY+MKF+   +D +VV +FL AA+VGILCKKNASISGAEVGCQGEVGSACAMAAAGLA+
Sbjct: 301 LHYFMKFSEAVTDANVVDYFLGAAAVGILCKKNASISGAEVGCQGEVGSACAMAAAGLAE 360

Query: 361 VLGATPEQLENAAEIGLEHNLGLTCDPVGGLVQVPCIERNAIAAVKAINATQMALRGDGK 420
           +LGATPEQL NAAEIGLEHNLGLTCDPVGGLVQVPCIERNAIAAVKAINA QMALRGDG+
Sbjct: 361 ILGATPEQLCNAAEIGLEHNLGLTCDPVGGLVQVPCIERNAIAAVKAINAAQMALRGDGQ 420

Query: 421 HFISLDRVIRTMRDTGADMHDKYKETSRGGLAVSWVEC 458
           HFISLDRVIRTMRDTGADMHDKYKETSRGGLAVS VEC
Sbjct: 421 HFISLDRVIRTMRDTGADMHDKYKETSRGGLAVSAVEC 458


Lambda     K      H
   0.319    0.134    0.399 

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: 687
Number of extensions: 25
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: 458
Length of database: 458
Length adjustment: 33
Effective length of query: 425
Effective length of database: 425
Effective search space:   180625
Effective search space used:   180625
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: 51 (24.3 bits)

Align candidate PfGW456L13_1089 (L-serine dehydratase (EC 4.3.1.17))
to HMM TIGR00720 (L-serine ammonia-lyase (EC 4.3.1.17))

# 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/TIGR00720.hmm
# target sequence database:        /tmp/gapView.14902.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00720  [M=450]
Accession:   TIGR00720
Description: sda_mono: L-serine ammonia-lyase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   3.1e-212  691.3   0.0   3.6e-212  691.1   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1089  L-serine dehydratase (EC 4.3.1.1


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1089  L-serine dehydratase (EC 4.3.1.17)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  691.1   0.0  3.6e-212  3.6e-212       1     449 [.       3     454 ..       3     455 .. 0.98

  Alignments for each domain:
  == domain 1  score: 691.1 bits;  conditional E-value: 3.6e-212
                                               TIGR00720   1 isvfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslalt 55 
                                                             isvfdlfkiGiGPssshtvGPm+aa+ fv+ l+++g leqv+rv+v+l+Gsl++t
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1089   3 ISVFDLFKIGIGPSSSHTVGPMRAAALFVQGLRERGLLEQVRRVEVQLFGSLSAT 57 
                                                             79***************************************************** PP

                                               TIGR00720  56 GkGhktdkavllGleGelpeevdiesieklleeveeekklklanqkeikfdlekd 110
                                                             G Gh++d+av++Gl+Ge p+ +d  +i   +++++e+++l l ++  + f   +d
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1089  58 GIGHGSDNAVIMGLMGEWPDAIDPSQIGICIANLRETDTLLLDGRLPVPFIWGRD 112
                                                             ******************************************************* PP

                                               TIGR00720 111 lafkdevlplhenglrlkaydeegevlkektyysvGGGfivdeeelkkeeeeee. 164
                                                             +++ de+lp+h+n+++l +  ++   l+++tyysvGGGf+vde+++++   + + 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1089 113 MRLIDENLPFHPNAMTLIVEGDD-GELHRDTYYSVGGGFVVDEAQASSGVVDLDs 166
                                                             *****************876666.789******************9988877664 PP

                                               TIGR00720 165 .evpypfksaaellelCkeeglsisevvlenekalrseeevraklleiwkvmeec 218
                                                               +py+f+saaellelCk+++l ++e++++ne ++rse+e+r+ l+++w++m++c
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1089 167 tVLPYDFSSAAELLELCKKHNLRVAELMMANERVWRSEDEIRSGLMKLWRAMQDC 221
                                                             478**************************************************** PP

                                               TIGR00720 219 ierglkaegvlpGglkvkrraaslkrklkakeets..kdplavldwvnlyalavn 271
                                                             +e+glk+eg+lpGgl+v+rraa+l+r l++ ++ +   ++l++++wvnl+alavn
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1089 222 VEQGLKHEGILPGGLNVRRRAAKLHRSLQELNKPNviGSTLSAMEWVNLFALAVN 276
                                                             ******************************9999877899*************** PP

                                               TIGR00720 272 eenaaGgrvvtaPtnGaagiiPavlayykkfveeaseekvvrflltagaiGilyk 326
                                                             eenaaGgr+vtaPtnGaagiiPavl+y+ kf e +++ +vv+++l a+a+Gil+k
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1089 277 EENAAGGRMVTAPTNGAAGIIPAVLHYFMKFSEAVTDANVVDYFLGAAAVGILCK 331
                                                             ******************************************************* PP

                                               TIGR00720 327 enasisgaevGCqgevGvacsmaaaglaellggtpeqvenaaeiamehnlGltCd 381
                                                             +nasisgaevGCqgevG+ac+maaaglae+lg+tpeq++naaei++ehnlGltCd
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1089 332 KNASISGAEVGCQGEVGSACAMAAAGLAEILGATPEQLCNAAEIGLEHNLGLTCD 386
                                                             ******************************************************* PP

                                               TIGR00720 382 PvgGlvqiPCiernaiaavkainaarlalkedgkkkvsldkvietmretGkdmka 436
                                                             PvgGlvq+PCiernaiaavkainaa++al++dg++++sld+vi+tmr+tG+dm+ 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1089 387 PVGGLVQVPCIERNAIAAVKAINAAQMALRGDGQHFISLDRVIRTMRDTGADMHD 441
                                                             ******************************************************* PP

                                               TIGR00720 437 kyketskgGlavk 449
                                                             kykets+gGlav+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1089 442 KYKETSRGGLAVS 454
                                                             ***********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (450 nodes)
Target sequences:                          1  (458 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.31
//
[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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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