GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__BFirm:BPHYT_RS02085
          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.

Links

Downloads

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:

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:

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:

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:

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