Alignments for a candidate for sdaB in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdaB in Pseudomonas putida KT2440

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate PP_0987 PP_0987 L-serine dehydratase

Query= reanno::pseudo6_N2E2:Pf6N2E2_5557
         (458 letters)



>FitnessBrowser__Putida:PP_0987
          Length = 458

 Score =  813 bits (2100), Expect = 0.0
 Identities = 406/458 (88%), Positives = 429/458 (93%)

Query: 1   MSLSVFDLFKIGIGPSSSHTVGPMRAAARFAEGLRRDDLLNCTTSVKVELYGSLGATGKG 60
           MSLSVFDLFKIGIGPSSSHTVGPMRAAARFAEGLRRD LL  T SVK ELYGSLGATGKG
Sbjct: 1   MSLSVFDLFKIGIGPSSSHTVGPMRAAARFAEGLRRDGLLARTASVKAELYGSLGATGKG 60

Query: 61  HGSDKAVLLGLEGEHPDTVDTETVDARLQAIRSSGRLNLLGEHSIEFNEKLHLAMIRKPL 120
           HGSDKAVLLGLEGEHPD +DT+++ ARLQ IR SG +NLLGEHSI F EK HLAMIRKPL
Sbjct: 61  HGSDKAVLLGLEGEHPDIIDTDSIPARLQVIRDSGHINLLGEHSIAFIEKQHLAMIRKPL 120

Query: 121 AFHPNGMIFRAFDAAGLQVRSREYYSVGGGFVVDEGAAGADRIVEDATPLTFPFKSAKDL 180
            +HPNGMIFRAFD AGLQ+RSREYYSVGGGFVVDE AAG DRIVED T L +PFK+AK L
Sbjct: 121 DYHPNGMIFRAFDDAGLQIRSREYYSVGGGFVVDEDAAGHDRIVEDTTVLAYPFKTAKAL 180

Query: 181 LGHCSTYGLSISQVMLTNESAWRPEAETRAGLLKIWQVMQDCVAAGCRNEGILPGGLKVK 240
           LGHC+ + LS+SQVML NESAWRPEAETRAGLL+IWQVMQDCVAAGC++EGILPGGLKVK
Sbjct: 181 LGHCTAHDLSVSQVMLANESAWRPEAETRAGLLRIWQVMQDCVAAGCQHEGILPGGLKVK 240

Query: 241 RRAAALHRQLCKNPEAALRDPLSVLDWVNLYALAVNEENAYGGRVVTAPTNGAAGIIPAV 300
           RRA AL+RQL  +PEA+LRD LSVLDWVNLYALAVNEENAYGGRVVTAPTNGAAGI+PAV
Sbjct: 241 RRAPALYRQLSGHPEASLRDALSVLDWVNLYALAVNEENAYGGRVVTAPTNGAAGIVPAV 300

Query: 301 LHYYMRFIPGASEDGVVRFLLTAAAIGILYKENASISGAEVGCQGEVGVACSMAAGALCE 360
           LHYYMRF+PGASEDGVVRFLLTAAAIGILYKENASISGAEVGCQGEVGVACSMAAGALCE
Sbjct: 301 LHYYMRFVPGASEDGVVRFLLTAAAIGILYKENASISGAEVGCQGEVGVACSMAAGALCE 360

Query: 361 VLGGSVQQVENAAEIGMEHNLGLTCDPIGGLVQVPCIERNAMGSVKAINAVRMAMRGDGH 420
           V+GGSVQQVENAAEIGMEHNLGLTCDPIGGLVQVPCIERNAMGSVKAINAVRMA+RGDG 
Sbjct: 361 VMGGSVQQVENAAEIGMEHNLGLTCDPIGGLVQVPCIERNAMGSVKAINAVRMALRGDGQ 420

Query: 421 HFVSLDKVIRTMRQTGADMKSKYKETARGGLAVNIIEC 458
           H+VSLDKVIRTMRQTGADMKSKYKETARGGLAVNIIEC
Sbjct: 421 HYVSLDKVIRTMRQTGADMKSKYKETARGGLAVNIIEC 458


Lambda     K      H
   0.320    0.136    0.401 

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: 829
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 PP_0987 PP_0987 (L-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.25142.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   6.7e-220  716.5   0.1   7.7e-220  716.4   0.1    1.0  1  lcl|FitnessBrowser__Putida:PP_0987  PP_0987 L-serine dehydratase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_0987  PP_0987 L-serine dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  716.4   0.1  7.7e-220  7.7e-220       2     450 .]       4     455 ..       3     455 .. 0.99

  Alignments for each domain:
  == domain 1  score: 716.4 bits;  conditional E-value: 7.7e-220
                           TIGR00720   2 svfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdkavllGleGelpee 76 
                                         svfdlfkiGiGPssshtvGPm+aa++f+e l++ g l+++++vk +lyGsl++tGkGh++dkavllGleGe+p+ 
  lcl|FitnessBrowser__Putida:PP_0987   4 SVFDLFKIGIGPSSSHTVGPMRAAARFAEGLRRDGLLARTASVKAELYGSLGATGKGHGSDKAVLLGLEGEHPDI 78 
                                         9************************************************************************** PP

                           TIGR00720  77 vdiesieklleeveeekklklanqkeikfdlekdlafkdevlplhenglrlkaydeegevlkektyysvGGGfiv 151
                                         +d++si+++l+ ++++++++l+++++i f ++++la+ ++ l++h+ng+ ++a+d++g ++++++yysvGGGf+v
  lcl|FitnessBrowser__Putida:PP_0987  79 IDTDSIPARLQVIRDSGHINLLGEHSIAFIEKQHLAMIRKPLDYHPNGMIFRAFDDAGLQIRSREYYSVGGGFVV 153
                                         *************************************************************************** PP

                           TIGR00720 152 deeelkkeeeeee..evpypfksaaellelCkeeglsisevvlenekalrseeevraklleiwkvmeecierglk 224
                                         de+++++++  e+   ++ypfk+a+ ll +C++++ls+s+v+l+ne a+r+e+e+ra ll+iw+vm++c+  g++
  lcl|FitnessBrowser__Putida:PP_0987 154 DEDAAGHDRIVEDttVLAYPFKTAKALLGHCTAHDLSVSQVMLANESAWRPEAETRAGLLRIWQVMQDCVAAGCQ 228
                                         ****9998765554488********************************************************** PP

                           TIGR00720 225 aegvlpGglkvkrraaslkrklkakeets.kdplavldwvnlyalavneenaaGgrvvtaPtnGaagiiPavlay 298
                                         +eg+lpGglkvkrra++l+r+l+ + e+s +d l+vldwvnlyalavneena GgrvvtaPtnGaagi+Pavl+y
  lcl|FitnessBrowser__Putida:PP_0987 229 HEGILPGGLKVKRRAPALYRQLSGHPEASlRDALSVLDWVNLYALAVNEENAYGGRVVTAPTNGAAGIVPAVLHY 303
                                         ***************************999********************************************* PP

                           TIGR00720 299 ykkfveeaseekvvrflltagaiGilykenasisgaevGCqgevGvacsmaaaglaellggtpeqvenaaeiame 373
                                         y +fv+ ase+ vvrfllta+aiGilykenasisgaevGCqgevGvacsmaa++l+e++gg+++qvenaaei+me
  lcl|FitnessBrowser__Putida:PP_0987 304 YMRFVPGASEDGVVRFLLTAAAIGILYKENASISGAEVGCQGEVGVACSMAAGALCEVMGGSVQQVENAAEIGME 378
                                         *************************************************************************** PP

                           TIGR00720 374 hnlGltCdPvgGlvqiPCiernaiaavkainaarlalkedgkkkvsldkvietmretGkdmkakyketskgGlav 448
                                         hnlGltCdP+gGlvq+PCierna+++vkaina r+al++dg+++vsldkvi+tmr+tG+dmk+kyket++gGlav
  lcl|FitnessBrowser__Putida:PP_0987 379 HNLGLTCDPIGGLVQVPCIERNAMGSVKAINAVRMALRGDGQHYVSLDKVIRTMRQTGADMKSKYKETARGGLAV 453
                                         *************************************************************************** PP

                           TIGR00720 449 kv 450
                                         ++
  lcl|FitnessBrowser__Putida:PP_0987 454 NI 455
                                         96 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: 7.78
//
[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