Alignments for a candidate for sdaB in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdaB in Burkholderia phytofirmans PsJN

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate BPHYT_RS19340 BPHYT_RS19340 serine dehydratase

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



>FitnessBrowser__BFirm:BPHYT_RS19340
          Length = 462

 Score =  919 bits (2374), Expect = 0.0
 Identities = 462/462 (100%), Positives = 462/462 (100%)

Query: 1   MAVSVFDLFKIGIGPSSSHTVGPMRAALMFAQGLERDGLLAATASVKVELYGSLGATGKG 60
           MAVSVFDLFKIGIGPSSSHTVGPMRAALMFAQGLERDGLLAATASVKVELYGSLGATGKG
Sbjct: 1   MAVSVFDLFKIGIGPSSSHTVGPMRAALMFAQGLERDGLLAATASVKVELYGSLGATGKG 60

Query: 61  HGTDRGVMLGLMGDAPDTVDPDTIAQRLEGVRVSRKLALLGTHEVPFVQKDHISFYRQAL 120
           HGTDRGVMLGLMGDAPDTVDPDTIAQRLEGVRVSRKLALLGTHEVPFVQKDHISFYRQAL
Sbjct: 61  HGTDRGVMLGLMGDAPDTVDPDTIAQRLEGVRVSRKLALLGTHEVPFVQKDHISFYRQAL 120

Query: 121 PEHPNGLKLRALDAQGETLRESTYLSVGGGFVVTAGAPNTKVLSAVEQLPHAFRSGNELL 180
           PEHPNGLKLRALDAQGETLRESTYLSVGGGFVVTAGAPNTKVLSAVEQLPHAFRSGNELL
Sbjct: 121 PEHPNGLKLRALDAQGETLRESTYLSVGGGFVVTAGAPNTKVLSAVEQLPHAFRSGNELL 180

Query: 181 ALCESTGKSIAQLMWENERVWHTEEETRAGLLKIWDVMQSCVARGCGINNPDADGNLPGP 240
           ALCESTGKSIAQLMWENERVWHTEEETRAGLLKIWDVMQSCVARGCGINNPDADGNLPGP
Sbjct: 181 ALCESTGKSIAQLMWENERVWHTEEETRAGLLKIWDVMQSCVARGCGINNPDADGNLPGP 240

Query: 241 FQVKRRAPQLYRALSGNPELALRDPLSMIDWINLYAIAVNEENAAGGRVVTAPTNGAAGI 300
           FQVKRRAPQLYRALSGNPELALRDPLSMIDWINLYAIAVNEENAAGGRVVTAPTNGAAGI
Sbjct: 241 FQVKRRAPQLYRALSGNPELALRDPLSMIDWINLYAIAVNEENAAGGRVVTAPTNGAAGI 300

Query: 301 IPAVLHYYMRFMPGSNQQGVIDFLMTAAAIGILYKLNASISGAEVGCQGEVGVACSMAAG 360
           IPAVLHYYMRFMPGSNQQGVIDFLMTAAAIGILYKLNASISGAEVGCQGEVGVACSMAAG
Sbjct: 301 IPAVLHYYMRFMPGSNQQGVIDFLMTAAAIGILYKLNASISGAEVGCQGEVGVACSMAAG 360

Query: 361 ALAAVMGGTPRQVENAAEIGMEHNLGLTCDPVGGMVQIPCIERNAMASVKAVNAARMALR 420
           ALAAVMGGTPRQVENAAEIGMEHNLGLTCDPVGGMVQIPCIERNAMASVKAVNAARMALR
Sbjct: 361 ALAAVMGGTPRQVENAAEIGMEHNLGLTCDPVGGMVQIPCIERNAMASVKAVNAARMALR 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: 864
Number of extensions: 24
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 BPHYT_RS19340 BPHYT_RS19340 (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.1339.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   1.4e-215  702.3   0.1   1.7e-215  702.1   0.1    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS19340  BPHYT_RS19340 serine dehydratase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS19340  BPHYT_RS19340 serine dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  702.1   0.1  1.7e-215  1.7e-215       1     450 []       3     459 ..       3     459 .. 0.98

  Alignments for each domain:
  == domain 1  score: 702.1 bits;  conditional E-value: 1.7e-215
                                TIGR00720   1 isvfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdkavllGle 70 
                                              +svfdlfkiGiGPssshtvGPm+aa +f++ l++ g l+++++vkv+lyGsl++tGkGh+td+ v+lGl+
  lcl|FitnessBrowser__BFirm:BPHYT_RS19340   3 VSVFDLFKIGIGPSSSHTVGPMRAALMFAQGLERDGLLAATASVKVELYGSLGATGKGHGTDRGVMLGLM 72 
                                              69******************************************************************** PP

                                TIGR00720  71 Gelpeevdiesieklleeveeekklklanqkeikfdlekdlafkdevlplhenglrlkaydeegevlkek 140
                                              G  p++vd ++i ++le v+ ++kl+l++++e+ f ++++++f++++lp+h+ngl+l+a+d +ge+l+e+
  lcl|FitnessBrowser__BFirm:BPHYT_RS19340  73 GDAPDTVDPDTIAQRLEGVRVSRKLALLGTHEVPFVQKDHISFYRQALPEHPNGLKLRALDAQGETLRES 142
                                              ********************************************************************** PP

                                TIGR00720 141 tyysvGGGfivdeeelkkeeeeee.evpypfksaaellelCkeeglsisevvlenekalrseeevrakll 209
                                              ty svGGGf+v+  + +++  +++ ++p++f+s +ell+lC+++g+si++++ ene ++++eee+ra ll
  lcl|FitnessBrowser__BFirm:BPHYT_RS19340 143 TYLSVGGGFVVTAGAPNTKVLSAVeQLPHAFRSGNELLALCESTGKSIAQLMWENERVWHTEEETRAGLL 212
                                              ************99988887777669******************************************** PP

                                TIGR00720 210 eiwkvmeeciergl..k...aegvlpGglkvkrraaslkrklkakeets.kdplavldwvnlyalavnee 273
                                              +iw+vm++c+ rg+  +   a+g lpG+++vkrra++l+r l+ + e   +dpl+++dw+nlya+avnee
  lcl|FitnessBrowser__BFirm:BPHYT_RS19340 213 KIWDVMQSCVARGCgiNnpdADGNLPGPFQVKRRAPQLYRALSGNPELAlRDPLSMIDWINLYAIAVNEE 282
                                              ************9844244579************************9999******************** PP

                                TIGR00720 274 naaGgrvvtaPtnGaagiiPavlayykkfveeaseekvvrflltagaiGilykenasisgaevGCqgevG 343
                                              naaGgrvvtaPtnGaagiiPavl+yy +f++ ++++ v++fl+ta+aiGilyk nasisgaevGCqgevG
  lcl|FitnessBrowser__BFirm:BPHYT_RS19340 283 NAAGGRVVTAPTNGAAGIIPAVLHYYMRFMPGSNQQGVIDFLMTAAAIGILYKLNASISGAEVGCQGEVG 352
                                              ********************************************************************** PP

                                TIGR00720 344 vacsmaaaglaellggtpeqvenaaeiamehnlGltCdPvgGlvqiPCiernaiaavkainaarlalked 413
                                              vacsmaa++la+++ggtp+qvenaaei+mehnlGltCdPvgG+vqiPCierna+a+vka+naar+al++d
  lcl|FitnessBrowser__BFirm:BPHYT_RS19340 353 VACSMAAGALAAVMGGTPRQVENAAEIGMEHNLGLTCDPVGGMVQIPCIERNAMASVKAVNAARMALRGD 422
                                              ********************************************************************** PP

                                TIGR00720 414 gkkkvsldkvietmretGkdmkakyketskgGlavkv 450
                                              g+++vsld+vi+tmretG+dmk+kykets+gGlav++
  lcl|FitnessBrowser__BFirm:BPHYT_RS19340 423 GSHYVSLDSVIKTMRETGADMKTKYKETSRGGLAVNI 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 8.83
//
[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