GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdaB in Pseudomonas fluorescens FW300-N2E2

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate Pf6N2E2_4685 L-serine dehydratase (EC 4.3.1.17)

Query= reanno::pseudo1_N1B4:Pf1N1B4_1013
         (458 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4685
          Length = 458

 Score =  716 bits (1849), Expect = 0.0
 Identities = 355/458 (77%), Positives = 397/458 (86%)

Query: 1   MAISVFDLFKVGIGPSSSHTVGPMRAAATFAQALIDQHLLADVRRVEIRLYGSLSATGVG 60
           MAISVFDLFK+GIGPSSSHTVGPMRAAA F +AL  + LL DVRRVE++L+GSLSATG+G
Sbjct: 1   MAISVFDLFKIGIGPSSSHTVGPMRAAALFVEALKAKVLLNDVRRVEVQLFGSLSATGIG 60

Query: 61  HATDRACVMGLMGEWPDSIDPNSIDSRIQTLRETGELSLAGKSTIAFNWQRDLLLLDESL 120
           H +D A +MGLMGEWPD+IDP+ I  RI+ LRET  L L G+  + F W RD+ L+DE+L
Sbjct: 61  HGSDNAVIMGLMGEWPDAIDPSQIGPRIELLRETQTLLLDGRLPVPFVWSRDMRLIDENL 120

Query: 121 PYHPNAMSLTAFGETGELFEQTYYSVGGGFIIEAAEAESGIAPASDVVLPYDFSSAAELL 180
           P+HPNAM+L A G  GEL   TYYSVGGGF+++ A+A SG+       LPYDFSSA ELL
Sbjct: 121 PFHPNAMTLVAEGADGELHRDTYYSVGGGFVVDQAQASSGVVDLDSTELPYDFSSAEELL 180

Query: 181 KLCNQHGLRVSELMMANERAWRSDAEIRQGLLHIWSVMRECVEQGLRHEGILPGGLNVPR 240
           +LC  H LRV+ELM+ANE+ WRS+ EIR GL+ +W  M++CVEQGL+HEGILPGGLNV R
Sbjct: 181 ELCRTHNLRVAELMLANEKVWRSEEEIRSGLMKLWRAMQDCVEQGLKHEGILPGGLNVRR 240

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

Query: 301 LHYYMKFNPDASDDDVVAFFLGAAAVGILCKKNASISGAEVGCQGEVGSACAMAAAGLAD 360
           LHY+MKF+   +D +VV +FLGAAAVGILCKKNASISGAEVGCQGEVGSACAMAAAGLA+
Sbjct: 301 LHYFMKFSEAVTDANVVDYFLGAAAVGILCKKNASISGAEVGCQGEVGSACAMAAAGLAE 360

Query: 361 ILGATPEQLENAAEIGLEHNLGLTCDPVGGLVQVPCIERNAIAAVKAINATQMALRGDGK 420
           ILGATPEQL NAAEIGLEHNLGLTCDPVGGLVQVPCIERNAIAAVKAINA QMALRGDG+
Sbjct: 361 ILGATPEQLCNAAEIGLEHNLGLTCDPVGGLVQVPCIERNAIAAVKAINAAQMALRGDGQ 420

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


Lambda     K      H
   0.319    0.134    0.396 

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: 624
Number of extensions: 16
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 Pf6N2E2_4685 (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.3146.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   2.3e-212  691.7   0.0   2.7e-212  691.5   0.0    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4685  L-serine dehydratase (EC 4.3.1.1


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4685  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 !  691.5   0.0  2.7e-212  2.7e-212       1     449 [.       3     454 ..       3     455 .. 0.98

  Alignments for each domain:
  == domain 1  score: 691.5 bits;  conditional E-value: 2.7e-212
                                      TIGR00720   1 isvfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdka 64 
                                                    isvfdlfkiGiGPssshtvGPm+aa+ fve+lk k  l++v+rv+v+l+Gsl++tG Gh++d+a
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4685   3 ISVFDLFKIGIGPSSSHTVGPMRAAALFVEALKAKVLLNDVRRVEVQLFGSLSATGIGHGSDNA 66 
                                                    79************************************************************** PP

                                      TIGR00720  65 vllGleGelpeevdiesieklleeveeekklklanqkeikfdlekdlafkdevlplhenglrlk 128
                                                    v++Gl+Ge p+ +d  +i  ++e ++e+++l l ++  + f  ++d+++ de+lp+h+n+++l 
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4685  67 VIMGLMGEWPDAIDPSQIGPRIELLRETQTLLLDGRLPVPFVWSRDMRLIDENLPFHPNAMTLV 130
                                                    ***************************************************************9 PP

                                      TIGR00720 129 aydeegevlkektyysvGGGfivdeeelkkeeeeee..evpypfksaaellelCkeeglsisev 190
                                                    a   +   l+++tyysvGGGf+vd++++++   + +  e+py+f+sa+ellelC++++l ++e+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4685 131 AEGAD-GELHRDTYYSVGGGFVVDQAQASSGVVDLDstELPYDFSSAEELLELCRTHNLRVAEL 193
                                                    98888.6799***************99998877655569************************* PP

                                      TIGR00720 191 vlenekalrseeevraklleiwkvmeecierglkaegvlpGglkvkrraaslkrklkakeets. 253
                                                    +l+nek++rseee+r+ l+++w++m++c+e+glk+eg+lpGgl+v+rraa+l+r l++ ++ + 
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4685 194 MLANEKVWRSEEEIRSGLMKLWRAMQDCVEQGLKHEGILPGGLNVRRRAAKLHRSLQELNKPNv 257
                                                    **********************************************************999987 PP

                                      TIGR00720 254 .kdplavldwvnlyalavneenaaGgrvvtaPtnGaagiiPavlayykkfveeaseekvvrfll 316
                                                      ++l++++wvnl+alavneenaaGgr+vtaPtnGaagiiPavl+y+ kf e +++ +vv+++l
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4685 258 iGSTLSAMEWVNLFALAVNEENAAGGRMVTAPTNGAAGIIPAVLHYFMKFSEAVTDANVVDYFL 321
                                                    7899************************************************************ PP

                                      TIGR00720 317 tagaiGilykenasisgaevGCqgevGvacsmaaaglaellggtpeqvenaaeiamehnlGltC 380
                                                     a+a+Gil+k+nasisgaevGCqgevG+ac+maaaglae+lg+tpeq++naaei++ehnlGltC
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4685 322 GAAAVGILCKKNASISGAEVGCQGEVGSACAMAAAGLAEILGATPEQLCNAAEIGLEHNLGLTC 385
                                                    **************************************************************** PP

                                      TIGR00720 381 dPvgGlvqiPCiernaiaavkainaarlalkedgkkkvsldkvietmretGkdmkakyketskg 444
                                                    dPvgGlvq+PCiernaiaavkainaa++al++dg++++sld+vi+tmr+tG+dm+ kykets+g
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4685 386 DPVGGLVQVPCIERNAIAAVKAINAAQMALRGDGQHFISLDRVIRTMRDTGADMHDKYKETSRG 449
                                                    **************************************************************** PP

                                      TIGR00720 445 Glavk 449
                                                    Glav+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4685 450 GLAVS 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.05
# Mc/sec: 3.88
//
[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