Alignments for a candidate for sdaB in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdaB in Pseudomonas simiae WCS417

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate GFF5136 PS417_26310 serine dehydratase

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



>FitnessBrowser__WCS417:GFF5136
          Length = 458

 Score =  721 bits (1862), Expect = 0.0
 Identities = 356/458 (77%), Positives = 399/458 (87%)

Query: 1   MAISVFDLFKVGIGPSSSHTVGPMRAAATFAQALIDQHLLADVRRVEIRLYGSLSATGVG 60
           MAISVFDLFK+GIGPSSSHTVGPMRAAA F QAL ++ LL  VRRVE++LYGSLSATG+G
Sbjct: 1   MAISVFDLFKIGIGPSSSHTVGPMRAAALFVQALRERELLEQVRRVEVQLYGSLSATGIG 60

Query: 61  HATDRACVMGLMGEWPDSIDPNSIDSRIQTLRETGELSLAGKSTIAFNWQRDLLLLDESL 120
           H +D A +MGLMGEWPD+IDP+ I  RI TLRET  L L G+  + F W RD+ LLDE+L
Sbjct: 61  HGSDTATIMGLMGEWPDAIDPSQIGQRIHTLRETDTLLLDGRLLVPFVWARDMRLLDENL 120

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

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

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

Query: 301 LHYYMKFNPDASDDDVVAFFLGAAAVGILCKKNASISGAEVGCQGEVGSACAMAAAGLAD 360
           LHY+MKF+ + ++ +VV + LGAAAVGILCKKNASISGAEVGCQGEVGSACAMAAAGLA+
Sbjct: 301 LHYFMKFSEEVTEANVVDYLLGAAAVGILCKKNASISGAEVGCQGEVGSACAMAAAGLAE 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: 630
Number of extensions: 17
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 GFF5136 PS417_26310 (serine dehydratase)
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.31550.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   6.6e-214  696.8   0.1   7.7e-214  696.6   0.1    1.0  1  lcl|FitnessBrowser__WCS417:GFF5136  PS417_26310 serine dehydratase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF5136  PS417_26310 serine dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  696.6   0.1  7.7e-214  7.7e-214       1     449 [.       3     454 ..       3     455 .. 0.98

  Alignments for each domain:
  == domain 1  score: 696.6 bits;  conditional E-value: 7.7e-214
                           TIGR00720   1 isvfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdkavllGleGelpe 75 
                                         isvfdlfkiGiGPssshtvGPm+aa+ fv++l++++ leqv+rv+v+lyGsl++tG Gh++d+a ++Gl+Ge p+
  lcl|FitnessBrowser__WCS417:GFF5136   3 ISVFDLFKIGIGPSSSHTVGPMRAAALFVQALRERELLEQVRRVEVQLYGSLSATGIGHGSDTATIMGLMGEWPD 77 
                                         79************************************************************************* PP

                           TIGR00720  76 evdiesieklleeveeekklklanqkeikfdlekdlafkdevlplhenglrlkaydeegevlkektyysvGGGfi 150
                                          +d  +i +++++++e+++l l ++  + f  ++d+++ de+lp+h+n+++l +  ++   l+++tyysvGGGf+
  lcl|FitnessBrowser__WCS417:GFF5136  78 AIDPSQIGQRIHTLRETDTLLLDGRLLVPFVWARDMRLLDENLPFHPNAMTLVVTGDH-GELHRDTYYSVGGGFV 151
                                         ****************************************************999888.6799************ PP

                           TIGR00720 151 vdeeelkkeeeeee..evpypfksaaellelCkeeglsisevvlenekalrseeevraklleiwkvmeeciergl 223
                                         vde+++++  ++ +  e+py+f+sa ell+lCk+++l ++e++l+nek++rseee+r+ l+++w++m++c+e+gl
  lcl|FitnessBrowser__WCS417:GFF5136 152 VDEAQAQSGVADMDrtELPYDFSSAVELLQLCKTHNLRVAELMLANEKTWRSEEEIRSGLMKLWRAMQDCVEQGL 226
                                         ***99988766555569********************************************************** PP

                           TIGR00720 224 kaegvlpGglkvkrraaslkrklkakeets..kdplavldwvnlyalavneenaaGgrvvtaPtnGaagiiPavl 296
                                         k+eg+lpGgl+v+rraa+l+r l++ ++ +   ++l++++wvnl+alavneenaaGgr+vtaPtnGaagiiPavl
  lcl|FitnessBrowser__WCS417:GFF5136 227 KHEGILPGGLNVRRRAAKLHRSLQELNKPNviGSTLSAMEWVNLFALAVNEENAAGGRMVTAPTNGAAGIIPAVL 301
                                         *************************9999877899**************************************** PP

                           TIGR00720 297 ayykkfveeaseekvvrflltagaiGilykenasisgaevGCqgevGvacsmaaaglaellggtpeqvenaaeia 371
                                         +y+ kf ee++e +vv++ll a+a+Gil+k+nasisgaevGCqgevG+ac+maaaglae+lg+tpeq++naaei+
  lcl|FitnessBrowser__WCS417:GFF5136 302 HYFMKFSEEVTEANVVDYLLGAAAVGILCKKNASISGAEVGCQGEVGSACAMAAAGLAEILGATPEQLCNAAEIG 376
                                         *************************************************************************** PP

                           TIGR00720 372 mehnlGltCdPvgGlvqiPCiernaiaavkainaarlalkedgkkkvsldkvietmretGkdmkakyketskgGl 446
                                         +ehnlGltCdPvgGlvq+PCiernaiaavkainaa++al++dg++++sld+vi+tmr+tG+dm+ kykets+gGl
  lcl|FitnessBrowser__WCS417:GFF5136 377 LEHNLGLTCDPVGGLVQVPCIERNAIAAVKAINAAQMALRGDGQHFISLDRVIRTMRDTGADMHDKYKETSRGGL 451
                                         *************************************************************************** PP

                           TIGR00720 447 avk 449
                                         av+
  lcl|FitnessBrowser__WCS417:GFF5136 452 AVS 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: 11.20
//
[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