Aligments for a candidate for mcmA in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Aligments for a candidate for mcmA in Burkholderia phytofirmans PsJN

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate BPHYT_RS02085 BPHYT_RS02085 methylmalonyl-CoA mutase

Query= BRENDA::Q8Y2U5
         (1099 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS02085 BPHYT_RS02085
            methylmalonyl-CoA mutase
          Length = 1298

 Score =  931 bits (2405), Expect = 0.0
 Identities = 473/608 (77%), Positives = 517/608 (85%), Gaps = 5/608 (0%)

Query: 492  LTALDAQAAERDARLGAAERKLLAMWPDLRRAYAGDEYVVKIRDRELRTPLTYTTLSGTT 551
            L  LD   A+R A LG  ER LL  WP    AY+G E++V+IRDRE+RT LT TTLSG+ 
Sbjct: 696  LQQLDTLIAQRTASLGERERALLDTWPQTVAAYSGAEHIVRIRDREIRTALTVTTLSGSE 755

Query: 552  LRKVVLPPYEDDGEILRWLMRENVPGSFPYTAGVFAFKRRGDVGGEDPTRMFAGEGDALR 611
            +RKV LP + D GEILRWLM +N+PG FP+TAGVF F+R      EDPTRMFAGEGD  R
Sbjct: 756  VRKVSLPKFADHGEILRWLMLDNLPGYFPFTAGVFPFRREN----EDPTRMFAGEGDPQR 811

Query: 612  TNRRFKLVSEGMEAKRLSTAFDSVTLYGEDPDPRPDIYGKVGNAGVSIATLDDLKVLYDG 671
            TNRRFKL+SEGM AKRLSTAFDSVTLYGE+PD RPDIYGKVGN+GVS+ATLDD+K LYDG
Sbjct: 812  TNRRFKLLSEGMPAKRLSTAFDSVTLYGEEPDERPDIYGKVGNSGVSVATLDDMKTLYDG 871

Query: 672  FDLTSPNTSVSMTINGPAPTILAMFMNTALDQNLARFRADNGREPTEGEEAKIRAWVLQN 731
            FDL +P TSVSMTINGPAPTILAMF N A+DQ +AR     GR  T  E +  R   L+N
Sbjct: 872  FDLCAPETSVSMTINGPAPTILAMFFNVAIDQQIARMTQQQGRPLTHDELSATRRAALEN 931

Query: 732  VRGTVQADILKEDQGQNTCIFSTAFSLKVMGDIQEYFVHHQVRNFYSVSISGYHIAEAGA 791
            VRGTVQADILKEDQGQNTCIFST FSLKVMGDIQ YFV H VRNFYSVSISGYHIAEAGA
Sbjct: 932  VRGTVQADILKEDQGQNTCIFSTEFSLKVMGDIQAYFVEHGVRNFYSVSISGYHIAEAGA 991

Query: 792  NPISQLAFTLANGFTYVEAYLARGMHIDDFAPNLSFFFSNGMDPEYSVLGRVARRIWAVT 851
            NPISQLA+TLANGFTYVEAYLARGM IDDFAPNLSFFFSNGMDPEY+VLGRVARRIWAV 
Sbjct: 992  NPISQLAYTLANGFTYVEAYLARGMSIDDFAPNLSFFFSNGMDPEYTVLGRVARRIWAVA 1051

Query: 852  MRDKYGANERSQKLKYHVQTSGRSLHAQEIAFNDIRTTLQALIAIYDNCNSLHTNAYDEA 911
            MR++YGANERSQKLKYHVQTSGRSLHAQEI FNDIRTTLQALIAIYDNCNSLHTNA+DEA
Sbjct: 1052 MRERYGANERSQKLKYHVQTSGRSLHAQEIDFNDIRTTLQALIAIYDNCNSLHTNAFDEA 1111

Query: 912  ITTPTAESVRRALAIQLIINREWGLAKCENPNQGSFIIDELTDLVEAAVLREFERLAERG 971
            ITTPT +SVRRA+AIQLIINREWGLAK +NPNQGSF+I+ELTDLVE AVL EF+RL ERG
Sbjct: 1112 ITTPTEDSVRRAVAIQLIINREWGLAKNQNPNQGSFVIEELTDLVEEAVLAEFDRLTERG 1171

Query: 972  GVLGAMETGYQRGRIQEESMLYEQRKHDGSLPIVGVNTFRNPEAGHAAPAHIELARSSEE 1031
            GVLGAMETGYQRGRIQ+ESMLYE RKHDGS PIVGVNTF +    H AP  I LARS+++
Sbjct: 1172 GVLGAMETGYQRGRIQDESMLYEHRKHDGSYPIVGVNTFLSAHP-HEAPQPIALARSTDD 1230

Query: 1032 EKQRQLARLADFHARHAAEAPAMLQRLQRAVIDDQNVFAVLMDAVRVCSLGQITHALFEV 1091
            EKQ QL RL  F ++H   APA L+RL+RAVIDD+NVFAVLMD VRVCSLGQITHALFEV
Sbjct: 1231 EKQSQLQRLRAFQSQHRDAAPAALERLKRAVIDDENVFAVLMDVVRVCSLGQITHALFEV 1290

Query: 1092 GGQYRRNM 1099
            GGQYRRNM
Sbjct: 1291 GGQYRRNM 1298



 Score =  396 bits (1017), Expect = e-114
 Identities = 223/348 (64%), Positives = 258/348 (74%), Gaps = 10/348 (2%)

Query: 161 AYAPTTLEPVAKGDRRALAQLITALESGRIDPALRQAVHARA---ATAHTPVLGITGTGG 217
           A    T +P +   RR LAQLI+A E+G +D + R+ + A+A   ATA TPVLGITGTGG
Sbjct: 271 ANTANTSDPASSTFRR-LAQLISAFEAGAVDASAREKLSAQAQAKATA-TPVLGITGTGG 328

Query: 218 AGKSSLTDELIRRFRLDQHDRLRIAVISIDPSRRKSGGALLGDRIRMNAINH----PNLF 273
           AGKSSLTDELIRRFRLD  D L IAV++IDPSRRKSGGALLGDRIRMNAI        ++
Sbjct: 329 AGKSSLTDELIRRFRLDYGDALTIAVLAIDPSRRKSGGALLGDRIRMNAIGDWGGGARVY 388

Query: 274 VRSLATREASSEISDALPDVIAACRAGGFDLIIVETSGIGQGDAAIVPHADLSLYVMTPE 333
           +RS+ATREASSE+SD+LPD +  C+A GFDLI+VETSGIGQG+AAIVP  D SLYVMTPE
Sbjct: 389 MRSMATREASSEVSDSLPDALMLCKAAGFDLIVVETSGIGQGNAAIVPFVDESLYVMTPE 448

Query: 334 FGAASQLEKIDMLDFADLVAINKFDRKGAQDAWRDVAKQVQRNREQWHAKPEDMPVFGTQ 393
           FGAASQLEKIDMLDFA  VAINKFDRKGA DA RDVAKQVQRNR  +   PE MPVFGT 
Sbjct: 449 FGAASQLEKIDMLDFAGFVAINKFDRKGAPDALRDVAKQVQRNRADFAKPPEAMPVFGTI 508

Query: 394 ASHFNDDGVTALYHALADRLAERGMALAERTLPRPAG-TCSTSHDAIVPPARVRYLAEVA 452
           AS FNDDGVTALY  +A+ L + G+      L  P G   S+  +AIVPPARVRYLA++A
Sbjct: 509 ASRFNDDGVTALYRHVAEALRKHGLRSGGGRLAAPEGLRFSSGRNAIVPPARVRYLADIA 568

Query: 453 DTVRGYHRRVDAQSGLARERQQLQASRRMLEAAGAAADVLTALDAQAA 500
            T+  Y  R DAQ+ LARER QL  +RRML  AG  A  +T   A A+
Sbjct: 569 QTIHAYRERADAQARLARERWQLVEARRMLGEAGTQAGAVTQSRASAS 616



 Score =  221 bits (563), Expect = 3e-61
 Identities = 152/364 (41%), Positives = 193/364 (53%), Gaps = 22/364 (6%)

Query: 1   MTDLSAARAAEPTSASEPGAVSNKVRFVTAASLFDGHDASINIMRRILQSMGCEVIHLGH 60
           MTDLS  + A     S       ++RFVTAA+LFDGHDASINIMRRILQ+ G EVIHLGH
Sbjct: 1   MTDLSTPQRA----GSHKLPAGRRLRFVTAAALFDGHDASINIMRRILQASGVEVIHLGH 56

Query: 61  NRSVDEVVNAALQEDVQGIAVSSYQGGHVEYFKYMIDALRARGGEHIQVFGGGGGVIVPA 120
           NRSVDEV  AALQED  G+AVSSYQGGH EYF+Y++D LRARGGE I+VFGGGGGVIVP 
Sbjct: 57  NRSVDEVATAALQEDADGVAVSSYQGGHNEYFRYLVDLLRARGGERIKVFGGGGGVIVPE 116

Query: 121 EIRELQDYGVARIYSPEDGQRMGLAGMIADMVRRCDIDLAAYAPT----TLEPVAKGDRR 176
           EI EL+ YGV +IYSP+DGQR+GL GMI DM+ RC     A          E V +  +R
Sbjct: 117 EISELESYGVEKIYSPQDGQRLGLQGMIDDMIARCAEGARAAEAVGQSRVGEWVDEFSKR 176

Query: 177 ALAQLITALESGRIDPALR----QAVHARAATAHTPVLGITGTGGAGKSSLT-DELIRRF 231
            L +  +  ++G  + A+R    QA H   AT+   V     T  A  ++ T D      
Sbjct: 177 GLPRFDSRGDAGGDEDAVRNPFSQASHVGCATSVGHVANAADTADAADTADTADAADTAD 236

Query: 232 RLDQHDRLRIAVISIDPSRRKSGGALLGDRIRMNAINHPNLFVRSLATREASSEISDALP 291
             D  D    A  +I  +   +           N  N  N    +  T + +S     L 
Sbjct: 237 AADTADTADTADTAIAANTANTANT-------ANTANTANT-ANTANTSDPASSTFRRLA 288

Query: 292 DVIAACRAGGFDLIIVE-TSGIGQGDAAIVPHADLSLYVMTPEFGAASQLEKIDMLDFAD 350
            +I+A  AG  D    E  S   Q  A   P   ++      +     +L +   LD+ D
Sbjct: 289 QLISAFEAGAVDASAREKLSAQAQAKATATPVLGITGTGGAGKSSLTDELIRRFRLDYGD 348

Query: 351 LVAI 354
            + I
Sbjct: 349 ALTI 352


Lambda     K      H
   0.320    0.134    0.388 

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: 3243
Number of extensions: 111
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 1099
Length of database: 1298
Length adjustment: 47
Effective length of query: 1052
Effective length of database: 1251
Effective search space:  1316052
Effective search space used:  1316052
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: 59 (27.3 bits)

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

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

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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 preprint on GapMind for carbon sources, or view the source code.

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