Alignments for a candidate for glcB in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for glcB in Burkholderia phytofirmans PsJN

Align Malate synthase (EC 2.3.3.9) (characterized)
to candidate BPHYT_RS12305 BPHYT_RS12305 malate synthase

Query= reanno::BFirm:BPHYT_RS12305
         (536 letters)



>FitnessBrowser__BFirm:BPHYT_RS12305
          Length = 536

 Score = 1074 bits (2777), Expect = 0.0
 Identities = 536/536 (100%), Positives = 536/536 (100%)

Query: 1   MASPQSSHSSLQLPQGMEITAEIKPGYDAILSREALELVAALHRTFEPRRQQLLQARAER 60
           MASPQSSHSSLQLPQGMEITAEIKPGYDAILSREALELVAALHRTFEPRRQQLLQARAER
Sbjct: 1   MASPQSSHSSLQLPQGMEITAEIKPGYDAILSREALELVAALHRTFEPRRQQLLQARAER 60

Query: 61  TKRLDAGERPDFLAETKSVRDGDWTIAPLPQDLQCRRVEITGPVERKMIINALNSGADSY 120
           TKRLDAGERPDFLAETKSVRDGDWTIAPLPQDLQCRRVEITGPVERKMIINALNSGADSY
Sbjct: 61  TKRLDAGERPDFLAETKSVRDGDWTIAPLPQDLQCRRVEITGPVERKMIINALNSGADSY 120

Query: 121 MTDFEDSNAPSWDNQITGHINLKDAVRRTISLEQNGKSYTLNDKVATLIVRPRGWHLDEK 180
           MTDFEDSNAPSWDNQITGHINLKDAVRRTISLEQNGKSYTLNDKVATLIVRPRGWHLDEK
Sbjct: 121 MTDFEDSNAPSWDNQITGHINLKDAVRRTISLEQNGKSYTLNDKVATLIVRPRGWHLDEK 180

Query: 181 HVKVDGKRVSGGIFDFALFMVHNAKELVARGSGPYFYLPKMESHLEARLWNDIFVAAQEA 240
           HVKVDGKRVSGGIFDFALFMVHNAKELVARGSGPYFYLPKMESHLEARLWNDIFVAAQEA
Sbjct: 181 HVKVDGKRVSGGIFDFALFMVHNAKELVARGSGPYFYLPKMESHLEARLWNDIFVAAQEA 240

Query: 241 VGVPRGTIRATVLIETIVAAFEMDEILYELREHSSGLNAGRWDYIFSAIKKFKADRDFCL 300
           VGVPRGTIRATVLIETIVAAFEMDEILYELREHSSGLNAGRWDYIFSAIKKFKADRDFCL
Sbjct: 241 VGVPRGTIRATVLIETIVAAFEMDEILYELREHSSGLNAGRWDYIFSAIKKFKADRDFCL 300

Query: 301 ADRSQITMTSPFMRAYALLLLKTCHRRNAPAIGGMSALIPIKNDPAANDKAMSGVRSDKA 360
           ADRSQITMTSPFMRAYALLLLKTCHRRNAPAIGGMSALIPIKNDPAANDKAMSGVRSDKA
Sbjct: 301 ADRSQITMTSPFMRAYALLLLKTCHRRNAPAIGGMSALIPIKNDPAANDKAMSGVRSDKA 360

Query: 361 RDAGDGYDGGWVAHPGLVPIAMEEFVKVLGDKPNQIGKQRDDVLVTATDLTDFRPEAPIT 420
           RDAGDGYDGGWVAHPGLVPIAMEEFVKVLGDKPNQIGKQRDDVLVTATDLTDFRPEAPIT
Sbjct: 361 RDAGDGYDGGWVAHPGLVPIAMEEFVKVLGDKPNQIGKQRDDVLVTATDLTDFRPEAPIT 420

Query: 421 EGGLRNNINVGIHYLGAWLAGNGCVPIHNLMEDAATAEISRSQVWQWIRSPKGKLEDGRK 480
           EGGLRNNINVGIHYLGAWLAGNGCVPIHNLMEDAATAEISRSQVWQWIRSPKGKLEDGRK
Sbjct: 421 EGGLRNNINVGIHYLGAWLAGNGCVPIHNLMEDAATAEISRSQVWQWIRSPKGKLEDGRK 480

Query: 481 VTAELVRELSAQELEKVKQAVGGDTKPYERAAQIFEEMSTSEQFTDFLTLPLYEEI 536
           VTAELVRELSAQELEKVKQAVGGDTKPYERAAQIFEEMSTSEQFTDFLTLPLYEEI
Sbjct: 481 VTAELVRELSAQELEKVKQAVGGDTKPYERAAQIFEEMSTSEQFTDFLTLPLYEEI 536


Lambda     K      H
   0.318    0.134    0.397 

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: 1000
Number of extensions: 20
Number of successful extensions: 3
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: 536
Length of database: 536
Length adjustment: 35
Effective length of query: 501
Effective length of database: 501
Effective search space:   251001
Effective search space used:   251001
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: 52 (24.6 bits)

Align candidate BPHYT_RS12305 BPHYT_RS12305 (malate synthase)
to HMM TIGR01344 (aceB: malate synthase A (EC 2.3.3.9))

# 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/TIGR01344.hmm
# target sequence database:        /tmp/gapView.7277.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01344  [M=511]
Accession:   TIGR01344
Description: malate_syn_A: malate synthase A
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   1.3e-238  778.3   0.0   1.4e-238  778.1   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS12305  BPHYT_RS12305 malate synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS12305  BPHYT_RS12305 malate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  778.1   0.0  1.4e-238  1.4e-238       1     510 [.      30     536 .]      30     536 .] 0.99

  Alignments for each domain:
  == domain 1  score: 778.1 bits;  conditional E-value: 1.4e-238
                                TIGR01344   1 vltkealeflaelhrrfaerrkellarrekkqakldkgelldflpetkeireddwkvaaipadlldrrve 70 
                                              +l++eale++a lhr+f++rr++ll++r+++  +ld+ge++dfl etk++r++dw++a++p+dl+ rrve
  lcl|FitnessBrowser__BFirm:BPHYT_RS12305  30 ILSREALELVAALHRTFEPRRQQLLQARAERTKRLDAGERPDFLAETKSVRDGDWTIAPLPQDLQCRRVE 99 
                                              7999****************************************************************** PP

                                TIGR01344  71 itGPvdrkmvinalnaeakvfladfedsssPtwenvveGqinlkdairgeidftdeesgkeyalkaklav 140
                                              itGPv+rkm+inaln++a  +++dfeds++P+w+n ++G inlkda+r++i+    ++gk+y+l+ k a+
  lcl|FitnessBrowser__BFirm:BPHYT_RS12305 100 ITGPVERKMIINALNSGADSYMTDFEDSNAPSWDNQITGHINLKDAVRRTISLE--QNGKSYTLNDKVAT 167
                                              ****************************************************98..7************* PP

                                TIGR01344 141 livrprGwhlkerhleidgkaisgslldfglyffhnarellkkGkGPyfylPkleshlearlwndvflla 210
                                              livrprGwhl e+h+++dgk +sg ++df+l++ hna+el+++G+GPyfylPk+eshlearlwnd+f+ a
  lcl|FitnessBrowser__BFirm:BPHYT_RS12305 168 LIVRPRGWHLDEKHVKVDGKRVSGGIFDFALFMVHNAKELVARGSGPYFYLPKMESHLEARLWNDIFVAA 237
                                              ********************************************************************** PP

                                TIGR01344 211 qevlglprGtikatvlietlpaafemdeilyelrehssGlncGrwdyifslikklkkaeevvlPdrdavt 280
                                              qe +g+prGti+atvliet+ aafemdeilyelrehssGln+Grwdyifs ikk+k + ++ l dr+++t
  lcl|FitnessBrowser__BFirm:BPHYT_RS12305 238 QEAVGVPRGTIRATVLIETIVAAFEMDEILYELREHSSGLNAGRWDYIFSAIKKFKADRDFCLADRSQIT 307
                                              ********************************************************************** PP

                                TIGR01344 281 mdkaflnaysklliqtchrrgafalGGmaafiPikddpaaneaalekvradkereaknGhdGtwvahPdl 350
                                              m+++f++ay+ ll++tchrr+a a+GGm+a iPik+dpaan++a++ vr+dk r+a +G+dG wvahP+l
  lcl|FitnessBrowser__BFirm:BPHYT_RS12305 308 MTSPFMRAYALLLLKTCHRRNAPAIGGMSALIPIKNDPAANDKAMSGVRSDKARDAGDGYDGGWVAHPGL 377
                                              ********************************************************************** PP

                                TIGR01344 351 vevalevfdevlge.pnqldrvrledvsitaaellev.kdasrteeGlrenirvglryieawlrGsGavp 418
                                              v++a+e f +vlg+ pnq+ ++r +dv +ta++l +  ++a  te Glr+ni+vg++y+ awl G+G+vp
  lcl|FitnessBrowser__BFirm:BPHYT_RS12305 378 VPIAMEEFVKVLGDkPNQIGKQR-DDVLVTATDLTDFrPEAPITEGGLRNNINVGIHYLGAWLAGNGCVP 446
                                              *************999*****88.9***********989******************************* PP

                                TIGR01344 419 iynlmedaataeisraqlwqwikhGv.vledGekvtselvrdllkeeleklkkesgkeeyakarleeaae 487
                                              i+nlmedaataeisr+q+wqwi+  +  ledG+kvt+elvr+l ++elek+k+++g +    + +e+aa+
  lcl|FitnessBrowser__BFirm:BPHYT_RS12305 447 IHNLMEDAATAEISRSQVWQWIRSPKgKLEDGRKVTAELVRELSAQELEKVKQAVGGDT---KPYERAAQ 513
                                              ***********************97636**************************99988...88****** PP

                                TIGR01344 488 llerlvlseeledfltlpaydel 510
                                              ++e++++se+++dfltlp+y+e+
  lcl|FitnessBrowser__BFirm:BPHYT_RS12305 514 IFEEMSTSEQFTDFLTLPLYEEI 536
                                              ********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (511 nodes)
Target sequences:                          1  (536 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: 12.27
//
[ok]

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

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Steps (tab-delimited)
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Protein sequences (fasta format)
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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