Alignments for a candidate for sdaB in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdaB in Paraburkholderia bryophila 376MFSha3.1

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate H281DRAFT_02407 H281DRAFT_02407 L-serine ammonia-lyase

Query= reanno::BFirm:BPHYT_RS19340
         (462 letters)



>FitnessBrowser__Burk376:H281DRAFT_02407
          Length = 462

 Score =  892 bits (2304), Expect = 0.0
 Identities = 445/462 (96%), Positives = 453/462 (98%)

Query: 1   MAVSVFDLFKIGIGPSSSHTVGPMRAALMFAQGLERDGLLAATASVKVELYGSLGATGKG 60
           MAVSVFDLFKIGIGPSSSHTVGPMRAALMFAQGLERDGLL  TASVK +LYGSLGATGKG
Sbjct: 1   MAVSVFDLFKIGIGPSSSHTVGPMRAALMFAQGLERDGLLPNTASVKADLYGSLGATGKG 60

Query: 61  HGTDRGVMLGLMGDAPDTVDPDTIAQRLEGVRVSRKLALLGTHEVPFVQKDHISFYRQAL 120
           HGTDRGVMLGLMGDAPDTVDPDTIAQRLE VR +RKLALLGTHEVPFVQKDHISFYRQAL
Sbjct: 61  HGTDRGVMLGLMGDAPDTVDPDTIAQRLEAVRTTRKLALLGTHEVPFVQKDHISFYRQAL 120

Query: 121 PEHPNGLKLRALDAQGETLRESTYLSVGGGFVVTAGAPNTKVLSAVEQLPHAFRSGNELL 180
           PEHPNGLKLRA D QGETLRESTYLSVGGGFVVTAGAPNTKVL+AV+QLPH+FR+GNELL
Sbjct: 121 PEHPNGLKLRAFDVQGETLRESTYLSVGGGFVVTAGAPNTKVLAAVDQLPHSFRTGNELL 180

Query: 181 ALCESTGKSIAQLMWENERVWHTEEETRAGLLKIWDVMQSCVARGCGINNPDADGNLPGP 240
           ALC STGKSIAQLMWENERVWHTEEETRAGLLKIWDVMQSCV+RGCGINNPDADGNLPGP
Sbjct: 181 ALCGSTGKSIAQLMWENERVWHTEEETRAGLLKIWDVMQSCVSRGCGINNPDADGNLPGP 240

Query: 241 FQVKRRAPQLYRALSGNPELALRDPLSMIDWINLYAIAVNEENAAGGRVVTAPTNGAAGI 300
           FQVKRRAPQLYRALSGNPELALRDPLSMIDWINLYAIAVNEENAAGGRVVTAPTNGAAGI
Sbjct: 241 FQVKRRAPQLYRALSGNPELALRDPLSMIDWINLYAIAVNEENAAGGRVVTAPTNGAAGI 300

Query: 301 IPAVLHYYMRFMPGSNQQGVIDFLMTAAAIGILYKLNASISGAEVGCQGEVGVACSMAAG 360
           IPAVLHYY RFMPGSNQQGVIDFLMTAAAIGILYKLNASISGAEVGCQGEVGVACSMAAG
Sbjct: 301 IPAVLHYYTRFMPGSNQQGVIDFLMTAAAIGILYKLNASISGAEVGCQGEVGVACSMAAG 360

Query: 361 ALAAVMGGTPRQVENAAEIGMEHNLGLTCDPVGGMVQIPCIERNAMASVKAVNAARMALR 420
           ALAAVMGGTP+QVENAAEIGMEHNLGLTCDPVGGMVQIPCIERNAMASVKAVNAARMALR
Sbjct: 361 ALAAVMGGTPKQVENAAEIGMEHNLGLTCDPVGGMVQIPCIERNAMASVKAVNAARMALR 420

Query: 421 GDGSHYVSLDSVIKTMRETGADMKTKYKETSRGGLAVNIVEC 462
           GDGSHYVSLDSVIKTMRETGADMKTKYKETSRGGLAVNIVEC
Sbjct: 421 GDGSHYVSLDSVIKTMRETGADMKTKYKETSRGGLAVNIVEC 462


Lambda     K      H
   0.318    0.134    0.394 

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: 857
Number of extensions: 28
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: 462
Length of database: 462
Length adjustment: 33
Effective length of query: 429
Effective length of database: 429
Effective search space:   184041
Effective search space used:   184041
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate H281DRAFT_02407 H281DRAFT_02407 (L-serine ammonia-lyase)
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.12873.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   4.9e-215  700.5   0.0   5.6e-215  700.3   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_02407  H281DRAFT_02407 L-serine ammonia


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_02407  H281DRAFT_02407 L-serine ammonia-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  700.3   0.0  5.6e-215  5.6e-215       1     450 []       3     459 ..       3     459 .. 0.98

  Alignments for each domain:
  == domain 1  score: 700.3 bits;  conditional E-value: 5.6e-215
                                    TIGR00720   1 isvfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdkavl 66 
                                                  +svfdlfkiGiGPssshtvGPm+aa +f++ l++ g l ++++vk dlyGsl++tGkGh+td+ v+
  lcl|FitnessBrowser__Burk376:H281DRAFT_02407   3 VSVFDLFKIGIGPSSSHTVGPMRAALMFAQGLERDGLLPNTASVKADLYGSLGATGKGHGTDRGVM 68 
                                                  69**************************************************************** PP

                                    TIGR00720  67 lGleGelpeevdiesieklleeveeekklklanqkeikfdlekdlafkdevlplhenglrlkayde 132
                                                  lGl+G  p++vd ++i ++le+v++++kl+l++++e+ f ++++++f++++lp+h+ngl+l+a+d 
  lcl|FitnessBrowser__Burk376:H281DRAFT_02407  69 LGLMGDAPDTVDPDTIAQRLEAVRTTRKLALLGTHEVPFVQKDHISFYRQALPEHPNGLKLRAFDV 134
                                                  ****************************************************************** PP

                                    TIGR00720 133 egevlkektyysvGGGfivdeeelkkeeeeee.evpypfksaaellelCkeeglsisevvleneka 197
                                                  +ge+l+e+ty svGGGf+v+  + +++   ++ ++p+ f++ +ell+lC ++g+si++++ ene +
  lcl|FitnessBrowser__Burk376:H281DRAFT_02407 135 QGETLRESTYLSVGGGFVVTAGAPNTKVLAAVdQLPHSFRTGNELLALCGSTGKSIAQLMWENERV 200
                                                  ********************99988887777669******************************** PP

                                    TIGR00720 198 lrseeevraklleiwkvmeeciergl..k...aegvlpGglkvkrraaslkrklkakeets.kdpl 257
                                                  +++eee+ra ll+iw+vm++c++rg+  +   a+g lpG+++vkrra++l+r l+ + e   +dpl
  lcl|FitnessBrowser__Burk376:H281DRAFT_02407 201 WHTEEETRAGLLKIWDVMQSCVSRGCgiNnpdADGNLPGPFQVKRRAPQLYRALSGNPELAlRDPL 266
                                                  ************************9844244579************************9999**** PP

                                    TIGR00720 258 avldwvnlyalavneenaaGgrvvtaPtnGaagiiPavlayykkfveeaseekvvrflltagaiGi 323
                                                  +++dw+nlya+avneenaaGgrvvtaPtnGaagiiPavl+yy++f++ ++++ v++fl+ta+aiGi
  lcl|FitnessBrowser__Burk376:H281DRAFT_02407 267 SMIDWINLYAIAVNEENAAGGRVVTAPTNGAAGIIPAVLHYYTRFMPGSNQQGVIDFLMTAAAIGI 332
                                                  ****************************************************************** PP

                                    TIGR00720 324 lykenasisgaevGCqgevGvacsmaaaglaellggtpeqvenaaeiamehnlGltCdPvgGlvqi 389
                                                  lyk nasisgaevGCqgevGvacsmaa++la+++ggtp+qvenaaei+mehnlGltCdPvgG+vqi
  lcl|FitnessBrowser__Burk376:H281DRAFT_02407 333 LYKLNASISGAEVGCQGEVGVACSMAAGALAAVMGGTPKQVENAAEIGMEHNLGLTCDPVGGMVQI 398
                                                  ****************************************************************** PP

                                    TIGR00720 390 PCiernaiaavkainaarlalkedgkkkvsldkvietmretGkdmkakyketskgGlavkv 450
                                                  PCierna+a+vka+naar+al++dg+++vsld+vi+tmretG+dmk+kykets+gGlav++
  lcl|FitnessBrowser__Burk376:H281DRAFT_02407 399 PCIERNAMASVKAVNAARMALRGDGSHYVSLDSVIKTMRETGADMKTKYKETSRGGLAVNI 459
                                                  ***********************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (450 nodes)
Target sequences:                          1  (462 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: 00:00:00.03
# Mc/sec: 6.77
//
[ok]

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

Downloads

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

Related tools

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