Alignments for a candidate for sdaB in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdaB in Pseudomonas fluorescens FW300-N1B4

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate Pf1N1B4_2423 L-serine dehydratase (EC 4.3.1.17)

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2423
          Length = 458

 Score =  731 bits (1886), Expect = 0.0
 Identities = 363/458 (79%), Positives = 405/458 (88%)

Query: 1   MAISVFDLFKVGIGPSSSHTVGPMRAAATFAQALFDQGLLEQTRRVEVRLYGSLSATGVG 60
           MAISVFDLFK+GIGPSSSHTVGPMRAAA F Q L +QGLLEQ RRVEV+LYGSLSATG+G
Sbjct: 1   MAISVFDLFKIGIGPSSSHTVGPMRAAALFVQGLREQGLLEQVRRVEVQLYGSLSATGIG 60

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

Query: 121 PYHPNAMSLTAFGESGQLWEQTYYSVGGGFIVEAAEAESGVPASSDVVLPYEFSSAVELL 180
           P+HPNAM+L A G+ G+L   TYYS+GGGF+V+ A+A SGV      VLPY+FSSAVELL
Sbjct: 121 PFHPNAMTLVAEGDHGELHRDTYYSIGGGFVVDEAQASSGVVDLDSTVLPYDFSSAVELL 180

Query: 181 SLCNQHGLRVSELMMANERAWRSDAEIRSGLLHIWSVMRECVEQGLRHEGILPGGLDVPR 240
           SLC QH LRV+ELMMANE+ WRS+ EIR+GL+ +W  M++CVEQGL+HEGILPGGL+V R
Sbjct: 181 SLCKQHNLRVAELMMANEKVWRSEEEIRAGLMKLWRAMQDCVEQGLKHEGILPGGLNVRR 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 LHYFMKFSEAVTDANVVDYFLSAAAVGILCKKNASISGAEVGCQGEVGSACAMAAAGLAE 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: 689
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 Pf1N1B4_2423 (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.437.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   1.1e-213  696.1   0.1   1.2e-213  695.9   0.1    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2423  L-serine dehydratase (EC 4.3.1.1


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2423  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 !  695.9   0.1  1.2e-213  1.2e-213       1     449 [.       3     454 ..       3     455 .. 0.98

  Alignments for each domain:
  == domain 1  score: 695.9 bits;  conditional E-value: 1.2e-213
                                      TIGR00720   1 isvfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdka 64 
                                                    isvfdlfkiGiGPssshtvGPm+aa+ fv+ l+++g leqv+rv+v+lyGsl++tG Gh++d+a
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2423   3 ISVFDLFKIGIGPSSSHTVGPMRAAALFVQGLREQGLLEQVRRVEVQLYGSLSATGIGHGSDNA 66 
                                                    79************************************************************** PP

                                      TIGR00720  65 vllGleGelpeevdiesieklleeveeekklklanqkeikfdlekdlafkdevlplhenglrlk 128
                                                    v++Gl+Ge p+ +d  +i  ++++++e+++l l ++ ++ f  ++d+++ de+lp+h+n+++l 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2423  67 VIMGLMGEWPDAIDPSQIGIRIAALRETDTLLLDGRLSVPFIWARDMRLIDENLPFHPNAMTLV 130
                                                    ***************************************************************9 PP

                                      TIGR00720 129 aydeegevlkektyysvGGGfivdeeelkkeeeeee..evpypfksaaellelCkeeglsisev 190
                                                    a  ++   l+++tyys+GGGf+vde+++++   + +   +py+f+sa ell+lCk+++l ++e+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2423 131 AEGDH-GELHRDTYYSIGGGFVVDEAQASSGVVDLDstVLPYDFSSAVELLSLCKQHNLRVAEL 193
                                                    98887.7799*****************9988877664478************************ PP

                                      TIGR00720 191 vlenekalrseeevraklleiwkvmeecierglkaegvlpGglkvkrraaslkrklkakeets. 253
                                                    +++nek++rseee+ra l+++w++m++c+e+glk+eg+lpGgl+v+rraa+l+r l++ ++ + 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2423 194 MMANEKVWRSEEEIRAGLMKLWRAMQDCVEQGLKHEGILPGGLNVRRRAAKLHRSLQELNKPNv 257
                                                    **********************************************************999987 PP

                                      TIGR00720 254 .kdplavldwvnlyalavneenaaGgrvvtaPtnGaagiiPavlayykkfveeaseekvvrfll 316
                                                      ++l++++wvnl+alavneenaaGgr+vtaPtnGaagiiPavl+y+ kf e +++ +vv+++l
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2423 258 iGSTLSAMEWVNLFALAVNEENAAGGRMVTAPTNGAAGIIPAVLHYFMKFSEAVTDANVVDYFL 321
                                                    7899************************************************************ PP

                                      TIGR00720 317 tagaiGilykenasisgaevGCqgevGvacsmaaaglaellggtpeqvenaaeiamehnlGltC 380
                                                    +a+a+Gil+k+nasisgaevGCqgevG+ac+maaaglae+lg+tpeq++naaei++ehnlGltC
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2423 322 SAAAVGILCKKNASISGAEVGCQGEVGSACAMAAAGLAEILGATPEQLCNAAEIGLEHNLGLTC 385
                                                    **************************************************************** PP

                                      TIGR00720 381 dPvgGlvqiPCiernaiaavkainaarlalkedgkkkvsldkvietmretGkdmkakyketskg 444
                                                    dPvgGlvq+PCiernaiaavkainaa++al++dg++++sld+vi+tmr+tG+dm+ kykets+g
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2423 386 DPVGGLVQVPCIERNAIAAVKAINAAQMALRGDGQHFISLDRVIRTMRDTGADMHDKYKETSRG 449
                                                    **************************************************************** PP

                                      TIGR00720 445 Glavk 449
                                                    Glav+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2423 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: 00:00:00.01
# Mc/sec: 11.38
//
[ok]

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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