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

GapMind for catabolism of small carbon sources

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

Align Malate synthase (EC 2.3.3.9) (characterized)
to candidate H281DRAFT_00576 H281DRAFT_00576 malate synthase

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



>FitnessBrowser__Burk376:H281DRAFT_00576
          Length = 533

 Score = 1018 bits (2632), Expect = 0.0
 Identities = 506/536 (94%), Positives = 520/536 (97%), Gaps = 3/536 (0%)

Query: 1   MASPQSSHSSLQLPQGMEITAEIKPGYDAILSREALELVAALHRTFEPRRQQLLQARAER 60
           MA+P SS   L LPQGMEITAEIKPGY+AIL+REALELVAALHRTFEPRRQQLLQAR ER
Sbjct: 1   MANPLSS---LSLPQGMEITAEIKPGYEAILTREALELVAALHRTFEPRRQQLLQARTER 57

Query: 61  TKRLDAGERPDFLAETKSVRDGDWTIAPLPQDLQCRRVEITGPVERKMIINALNSGADSY 120
           T RLDAGERPDFLA TKSVRDGDWTIAPLP+DL+CRRVEITGPVERKMIINALNSGADSY
Sbjct: 58  TNRLDAGERPDFLAATKSVRDGDWTIAPLPEDLKCRRVEITGPVERKMIINALNSGADSY 117

Query: 121 MTDFEDSNAPSWDNQITGHINLKDAVRRTISLEQNGKSYTLNDKVATLIVRPRGWHLDEK 180
           MTDFEDSNAPSWDNQITGH+NLKDAVRRTISLEQNGKSY LNDKVATLIVRPRGWHLDEK
Sbjct: 118 MTDFEDSNAPSWDNQITGHVNLKDAVRRTISLEQNGKSYKLNDKVATLIVRPRGWHLDEK 177

Query: 181 HVKVDGKRVSGGIFDFALFMVHNAKELVARGSGPYFYLPKMESHLEARLWNDIFVAAQEA 240
           HVKVDGKRVSGGIFDFALFM HNAKELVARGSGPYFYLPKMESHLEARLWNDIFVAAQEA
Sbjct: 178 HVKVDGKRVSGGIFDFALFMAHNAKELVARGSGPYFYLPKMESHLEARLWNDIFVAAQEA 237

Query: 241 VGVPRGTIRATVLIETIVAAFEMDEILYELREHSSGLNAGRWDYIFSAIKKFKADRDFCL 300
           VGVPRGTIRATVLIETI+AAFEMDEILYELREHSSGLNAGRWDYIFSAIKKFK+DRDFCL
Sbjct: 238 VGVPRGTIRATVLIETILAAFEMDEILYELREHSSGLNAGRWDYIFSAIKKFKSDRDFCL 297

Query: 301 ADRSQITMTSPFMRAYALLLLKTCHRRNAPAIGGMSALIPIKNDPAANDKAMSGVRSDKA 360
           ADRSQITMT+PFMRAYALLLLKTCHRRNAPAIGGMSALIPIKNDPAANDKAM+GVRSDKA
Sbjct: 298 ADRSQITMTAPFMRAYALLLLKTCHRRNAPAIGGMSALIPIKNDPAANDKAMAGVRSDKA 357

Query: 361 RDAGDGYDGGWVAHPGLVPIAMEEFVKVLGDKPNQIGKQRDDVLVTATDLTDFRPEAPIT 420
           RDAGDGYDGGWVAHPGLVPIAMEEFVKVLGDKPNQIGKQR DVLVTATDL DFRPEAPIT
Sbjct: 358 RDAGDGYDGGWVAHPGLVPIAMEEFVKVLGDKPNQIGKQRVDVLVTATDLMDFRPEAPIT 417

Query: 421 EGGLRNNINVGIHYLGAWLAGNGCVPIHNLMEDAATAEISRSQVWQWIRSPKGKLEDGRK 480
           E GLRNNINVGIHYLG+WLAGNGCVPIHNLMEDAATAEISRSQVWQWIRSPKG L+DGRK
Sbjct: 418 EAGLRNNINVGIHYLGSWLAGNGCVPIHNLMEDAATAEISRSQVWQWIRSPKGTLDDGRK 477

Query: 481 VTAELVRELSAQELEKVKQAVGGDTKPYERAAQIFEEMSTSEQFTDFLTLPLYEEI 536
           VTAELVREL+  EL+KVKQAVGGDTKPYERAAQIFEEMSTSEQFTDFLTLPLYEEI
Sbjct: 478 VTAELVRELAGHELDKVKQAVGGDTKPYERAAQIFEEMSTSEQFTDFLTLPLYEEI 533


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: 980
Number of extensions: 23
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: 533
Length adjustment: 35
Effective length of query: 501
Effective length of database: 498
Effective search space:   249498
Effective search space used:   249498
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 H281DRAFT_00576 H281DRAFT_00576 (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.31877.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   1.4e-237  774.8   0.0   1.6e-237  774.7   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_00576  H281DRAFT_00576 malate synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_00576  H281DRAFT_00576 malate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  774.7   0.0  1.6e-237  1.6e-237       1     510 [.      27     533 .]      27     533 .] 0.99

  Alignments for each domain:
  == domain 1  score: 774.7 bits;  conditional E-value: 1.6e-237
                                    TIGR01344   1 vltkealeflaelhrrfaerrkellarrekkqakldkgelldflpetkeireddwkvaaipadlld 66 
                                                  +lt+eale++a lhr+f++rr++ll++r+++  +ld+ge++dfl  tk++r++dw++a++p+dl+ 
  lcl|FitnessBrowser__Burk376:H281DRAFT_00576  27 ILTREALELVAALHRTFEPRRQQLLQARTERTNRLDAGERPDFLAATKSVRDGDWTIAPLPEDLKC 92 
                                                  89**************************************************************** PP

                                    TIGR01344  67 rrveitGPvdrkmvinalnaeakvfladfedsssPtwenvveGqinlkdairgeidftdeesgkey 132
                                                  rrveitGPv+rkm+inaln++a  +++dfeds++P+w+n ++G +nlkda+r++i+    ++gk+y
  lcl|FitnessBrowser__Burk376:H281DRAFT_00576  93 RRVEITGPVERKMIINALNSGADSYMTDFEDSNAPSWDNQITGHVNLKDAVRRTISLE--QNGKSY 156
                                                  ********************************************************98..7***** PP

                                    TIGR01344 133 alkaklavlivrprGwhlkerhleidgkaisgslldfglyffhnarellkkGkGPyfylPkleshl 198
                                                  +l+ k a+livrprGwhl e+h+++dgk +sg ++df+l++ hna+el+++G+GPyfylPk+eshl
  lcl|FitnessBrowser__Burk376:H281DRAFT_00576 157 KLNDKVATLIVRPRGWHLDEKHVKVDGKRVSGGIFDFALFMAHNAKELVARGSGPYFYLPKMESHL 222
                                                  ****************************************************************** PP

                                    TIGR01344 199 earlwndvfllaqevlglprGtikatvlietlpaafemdeilyelrehssGlncGrwdyifslikk 264
                                                  earlwnd+f+ aqe +g+prGti+atvliet+ aafemdeilyelrehssGln+Grwdyifs ikk
  lcl|FitnessBrowser__Burk376:H281DRAFT_00576 223 EARLWNDIFVAAQEAVGVPRGTIRATVLIETILAAFEMDEILYELREHSSGLNAGRWDYIFSAIKK 288
                                                  ****************************************************************** PP

                                    TIGR01344 265 lkkaeevvlPdrdavtmdkaflnaysklliqtchrrgafalGGmaafiPikddpaaneaalekvra 330
                                                  +k++ ++ l dr+++tm+++f++ay+ ll++tchrr+a a+GGm+a iPik+dpaan++a++ vr+
  lcl|FitnessBrowser__Burk376:H281DRAFT_00576 289 FKSDRDFCLADRSQITMTAPFMRAYALLLLKTCHRRNAPAIGGMSALIPIKNDPAANDKAMAGVRS 354
                                                  ****************************************************************** PP

                                    TIGR01344 331 dkereaknGhdGtwvahPdlvevalevfdevlge.pnqldrvrledvsitaaellev.kdasrtee 394
                                                  dk r+a +G+dG wvahP+lv++a+e f +vlg+ pnq+ ++r +dv +ta++l++  ++a  te+
  lcl|FitnessBrowser__Burk376:H281DRAFT_00576 355 DKARDAGDGYDGGWVAHPGLVPIAMEEFVKVLGDkPNQIGKQR-VDVLVTATDLMDFrPEAPITEA 419
                                                  *********************************999*****88.9***********989******* PP

                                    TIGR01344 395 GlrenirvglryieawlrGsGavpiynlmedaataeisraqlwqwikhGv.vledGekvtselvrd 459
                                                  Glr+ni+vg++y+ +wl G+G+vpi+nlmedaataeisr+q+wqwi+  + +l+dG+kvt+elvr+
  lcl|FitnessBrowser__Burk376:H281DRAFT_00576 420 GLRNNINVGIHYLGSWLAGNGCVPIHNLMEDAATAEISRSQVWQWIRSPKgTLDDGRKVTAELVRE 485
                                                  ***********************************************97648************** PP

                                    TIGR01344 460 llkeeleklkkesgkeeyakarleeaaellerlvlseeledfltlpaydel 510
                                                  l+ +el+k+k+++g +    + +e+aa+++e++++se+++dfltlp+y+e+
  lcl|FitnessBrowser__Burk376:H281DRAFT_00576 486 LAGHELDKVKQAVGGDT---KPYERAAQIFEEMSTSEQFTDFLTLPLYEEI 533
                                                  ************99988...88**************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (511 nodes)
Target sequences:                          1  (533 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.83
//
[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