Alignments for a candidate for glcB in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for glcB in Dyella japonica UNC79MFTsu3.2

Align malate synthase A (EC 2.3.3.9) (characterized)
to candidate N515DRAFT_4124 N515DRAFT_4124 malate synthase

Query= ecocyc::MALATE-SYNTHASE
         (533 letters)



>FitnessBrowser__Dyella79:N515DRAFT_4124
          Length = 543

 Score =  529 bits (1363), Expect = e-155
 Identities = 283/529 (53%), Positives = 347/529 (65%), Gaps = 18/529 (3%)

Query: 18  GEQEKQILTAEAVEFLTELVTHFTPQRNKLLAARIQQQQDIDNGTLPDFISETASIRDAD 77
           G   + ILT  A+ FL +L   F  +R  LLAAR  +Q   D G LPDF ++T +IR+  
Sbjct: 20  GPGHESILTPAALAFLADLHHRFNDRRLDLLAARRTRQARYDAGELPDFRADTLAIREGR 79

Query: 78  WKIRGIPADLEDRRVEITGPVERKMVINALNANVKVFMADFEDSLAPDWNKVIDGQINLR 137
           W +  IPA L+DRRVEITGPVERKM+INALN+  KVFMADFEDS AP      DGQINLR
Sbjct: 80  WTVGKIPAALQDRRVEITGPVERKMIINALNSGAKVFMADFEDSSAPTLANQFDGQINLR 139

Query: 138 DAVNGTISYTNEAGKIYQLKPNPAVLICRVRGLHLPEKHVTWRGEAIPGSLFDFALYFFH 197
           DAVNGTI YT+  GK Y++  +PAVL+ R RG HLPE+H+T  GE + G+L DF LY FH
Sbjct: 140 DAVNGTIGYTSPEGKTYRVGHDPAVLVVRPRGWHLPERHLTVDGEPMSGALVDFGLYAFH 199

Query: 198 NYQALLAKGSGPYFYLPKTQSWQEAAWWSEVFSYAEDRFNLPRGTIKATLLIETLPAVFQ 257
           N +AL A+  GPYFYLPK ++ +EAA W E  + AE+   LP   +KAT+LIETLPAVFQ
Sbjct: 200 NARALQARDRGPYFYLPKLEAMEEAALWHEAMAAAEEALGLPAHCMKATVLIETLPAVFQ 259

Query: 258 MDEILHALRDHIVGLNCGRWDYIFSYIKTLKNYPDRVLPDRQAVTMDKPFLNAYSRLLIK 317
           M EILHALR+  VGLNCGRWDYIFSY+KT + + DR+LP+R  V M  PFL AYS LLI+
Sbjct: 260 MHEILHALRERAVGLNCGRWDYIFSYLKTFRGHRDRLLPERGQVLMTVPFLKAYSELLIQ 319

Query: 318 TCHKRGAFAMGGMAAFIPSK-DEEHNNQVLNKVKADKSLEANNGHDGTWIAHPGLADTAM 376
           TCH+RGAFAMGGMAA IP K DE  N   L KV+ADK  E   GHDGTW+AHP L   A 
Sbjct: 320 TCHRRGAFAMGGMAAQIPIKGDEAANEAALAKVRADKLREVQAGHDGTWVAHPALVPVAR 379

Query: 377 AVFNDILGSRKNQLEVMREQDAPITADQLLAPCDGERTEEGMRANIRVAVQYIEAWISGN 436
            +F+  + S  NQL V R  D   + DQL+APC G  +  G   N+ VA++Y  AW+ G 
Sbjct: 380 EIFDQYMPS-PNQLNVAR-ADVQASRDQLIAPCAGTISRAGFDNNVEVALRYTAAWLDGL 437

Query: 437 GCVPIYGLMEDAATAEISRTSIWQWIHHQKTLSNG------------KPVTKALFRQMLG 484
           GCVPI+ LMEDAATAEI+R  +WQW+HH    + G             P+  ALF Q L 
Sbjct: 438 GCVPIHHLMEDAATAEIARAQLWQWLHHPGNPAGGTPAGDGLEFTDHAPIDFALFDQALA 497

Query: 485 EEMKVIASELGEERFSQGRFDDAARLMEQITTSDELIDFLTLPGYRLLA 533
                + +          R DDAA L+  +T +++L DFLTLP Y  LA
Sbjct: 498 AHTHRLRASTHP---GAARADDAAALLATLTHAEQLGDFLTLPAYDRLA 543


Lambda     K      H
   0.320    0.135    0.407 

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: 759
Number of extensions: 30
Number of successful extensions: 4
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: 533
Length of database: 543
Length adjustment: 35
Effective length of query: 498
Effective length of database: 508
Effective search space:   252984
Effective search space used:   252984
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: 52 (24.6 bits)

Align candidate N515DRAFT_4124 N515DRAFT_4124 (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.24045.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   4.1e-221  720.5   0.0   4.7e-221  720.3   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_4124  N515DRAFT_4124 malate synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_4124  N515DRAFT_4124 malate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  720.3   0.0  4.7e-221  4.7e-221       1     510 [.      26     542 ..      26     543 .] 0.95

  Alignments for each domain:
  == domain 1  score: 720.3 bits;  conditional E-value: 4.7e-221
                                    TIGR01344   1 vltkealeflaelhrrfaerrkellarrekkqakldkgelldflpetkeireddwkvaaipadlld 66 
                                                  +lt++al+fla+lh+rf++rr +lla+r+++qa++d+gel+df  +t +ire+ w+v +ipa+l+d
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4124  26 ILTPAALAFLADLHHRFNDRRLDLLAARRTRQARYDAGELPDFRADTLAIREGRWTVGKIPAALQD 91 
                                                  79**************************************************************** PP

                                    TIGR01344  67 rrveitGPvdrkmvinalnaeakvfladfedsssPtwenvveGqinlkdairgeidftdeesgkey 132
                                                  rrveitGPv+rkm+inaln++akvf+adfedss+Pt +n  +Gqinl+da++g+i +t+  +gk+y
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4124  92 RRVEITGPVERKMIINALNSGAKVFMADFEDSSAPTLANQFDGQINLRDAVNGTIGYTS-PEGKTY 156
                                                  **********************************************************6.88**** PP

                                    TIGR01344 133 alkaklavlivrprGwhlkerhleidgkaisgslldfglyffhnarellkkGkGPyfylPkleshl 198
                                                  ++  + avl+vrprGwhl+erhl++dg+++sg+l+dfgly+fhnar+l ++ +GPyfylPkle+  
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4124 157 RVGHDPAVLVVRPRGWHLPERHLTVDGEPMSGALVDFGLYAFHNARALQARDRGPYFYLPKLEAME 222
                                                  ****************************************************************** PP

                                    TIGR01344 199 earlwndvfllaqevlglprGtikatvlietlpaafemdeilyelrehssGlncGrwdyifslikk 264
                                                  ea lw + +  a+e lglp   +katvlietlpa+f+m+eil+ lre ++GlncGrwdyifs++k+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4124 223 EAALWHEAMAAAEEALGLPAHCMKATVLIETLPAVFQMHEILHALRERAVGLNCGRWDYIFSYLKT 288
                                                  ****************************************************************** PP

                                    TIGR01344 265 lkkaeevvlPdrdavtmdkaflnaysklliqtchrrgafalGGmaafiPikddpaaneaalekvra 330
                                                  ++ + +++lP+r +v m+ +fl+ays+lliqtchrrgafa+GGmaa+iPik+d+aaneaal+kvra
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4124 289 FRGHRDRLLPERGQVLMTVPFLKAYSELLIQTCHRRGAFAMGGMAAQIPIKGDEAANEAALAKVRA 354
                                                  ****************************************************************** PP

                                    TIGR01344 331 dkereaknGhdGtwvahPdlvevalevfdevlgepnqldrvrledvsitaaellevkdasrteeGl 396
                                                  dk re+++GhdGtwvahP+lv+va+e+fd+++++pnql++ r +dv+ ++ +l++ ++++ + +G+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4124 355 DKLREVQAGHDGTWVAHPALVPVAREIFDQYMPSPNQLNVAR-ADVQASRDQLIAPCAGTISRAGF 419
                                                  ****************************************99.9********************** PP

                                    TIGR01344 397 renirvglryieawlrGsGavpiynlmedaataeisraqlwqwikh......GvvledGekvts.. 454
                                                   +n++v+lry++awl+G G+vpi++lmedaataei+raqlwqw++h      G+   dG + t   
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4124 420 DNNVEVALRYTAAWLDGLGCVPIHHLMEDAATAEIARAQLWQWLHHpgnpagGTPAGDGLEFTDha 485
                                                  ********************************************9876666544455565555411 PP

                                    TIGR01344 455 ....elvrdllkeeleklkkesgkeeyakarleeaaellerlvlseeledfltlpaydel 510
                                                      +l+ ++l+  +++l+ +    + ++ar + aa ll  l+ +e+l dfltlpayd+l
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4124 486 pidfALFDQALAAHTHRLRAS---THPGAARADDAAALLATLTHAEQLGDFLTLPAYDRL 542
                                                  111167777777777777766...455789****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (511 nodes)
Target sequences:                          1  (543 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: 7.90
//
[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