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

GapMind for catabolism of small carbon sources

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

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate H281DRAFT_02110 H281DRAFT_02110 methylmalonyl-CoA mutase

Query= BRENDA::Q8Y2U5
         (1099 letters)



>FitnessBrowser__Burk376:H281DRAFT_02110
          Length = 1132

 Score = 1521 bits (3938), Expect = 0.0
 Identities = 811/1141 (71%), Positives = 898/1141 (78%), Gaps = 51/1141 (4%)

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

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

Query: 121  EIRELQDYGVARIYSPEDGQRMGLAGMIADMVRRCDI----DLAA--------YAPTTLE 168
            EI  L++YGV +IYSP DGQR+GL GMI DM+ RC      D  A         A  T +
Sbjct: 117  EIVALENYGVEKIYSPHDGQRLGLQGMIDDMIARCSAAAREDATARTGAVGEWLASVTGQ 176

Query: 169  PV--------AKGDR-------------RALAQLITALESGRIDPALRQAVHARAATAHT 207
            P+         +G+              R LAQLI+A E+G +  + R  + A       
Sbjct: 177  PLLHLRSSAQVRGETSSADSLDASSLVFRRLAQLISAFETGGVASSKRAELSALTQAVQV 236

Query: 208  PVLGITGTGGAGKSSLTDELIRRFRLDQHDRLRIAVISIDPSRRKSGGALLGDRIRMNAI 267
            PVLGITGTGGAGKSSLTDELIRRFRLD  D L IAV++IDPSRRKSGGALLGDRIRMNAI
Sbjct: 237  PVLGITGTGGAGKSSLTDELIRRFRLDYGDTLTIAVLAIDPSRRKSGGALLGDRIRMNAI 296

Query: 268  NH----PNLFVRSLATREASSEISDALPDVIAACRAGGFDLIIVETSGIGQGDAAIVPHA 323
                    +++RS+ATREASSEISDALPD +  C+A GFDLI+VETSGIGQGDAAIVP  
Sbjct: 297  GDWGGGARVYMRSMATREASSEISDALPDALMLCKAAGFDLIVVETSGIGQGDAAIVPFV 356

Query: 324  DLSLYVMTPEFGAASQLEKIDMLDFADLVAINKFDRKGAQDAWRDVAKQVQRNREQWHAK 383
            D SLYVMTPEFGAASQLEKIDMLDFAD VAIN+FDRKGA DA RDVAKQVQRNR  +   
Sbjct: 357  DESLYVMTPEFGAASQLEKIDMLDFADAVAINRFDRKGAPDALRDVAKQVQRNRADFAKS 416

Query: 384  PEDMPVFGTQASHFNDDGVTALYHALADRLAERGMALAERTLPRPAGT-CSTSHDAIVPP 442
            PE MPVFGT ASHFNDDGVTALY  +A+ L + G+      L   A    S+   AIVPP
Sbjct: 417  PEAMPVFGTIASHFNDDGVTALYQYIAEALRKHGLRSGGGRLSIAADVRFSSGRHAIVPP 476

Query: 443  ARVRYLAEVADTVRGYHRRVDAQSGLARERQQLQASRRML-EAAGAAADV---LTALDAQ 498
            ARVRYLAE+A T+  Y  RVD Q+G+ARER QL  +RRML EA+  A D    L +LDA 
Sbjct: 477  ARVRYLAEIAQTIHAYRERVDQQAGVARERWQLVEARRMLGEASADAHDAQASLASLDAL 536

Query: 499  AAERDARLGAAERKLLAMWPDLRRAYAGDEYVVKIRDRELRTPLTYTTLSGTTLRKVVLP 558
              +R   LG  ERKLL  WP    AY+GD++VV+IRDRE+RT LT TTLSGT LRKV LP
Sbjct: 537  IEQRTTALGEHERKLLDAWPQTVAAYSGDDHVVRIRDREIRTALTATTLSGTQLRKVALP 596

Query: 559  PYEDDGEILRWLMRENVPGSFPYTAGVFAFKRRGDVGGEDPTRMFAGEGDALRTNRRFKL 618
             + D GEILRWLM +N+PG FP+TAGVF F+R      EDPTRMFAGEGD  RTNRRFKL
Sbjct: 597  KFVDHGEILRWLMLDNLPGYFPFTAGVFPFRREN----EDPTRMFAGEGDPSRTNRRFKL 652

Query: 619  VSEGMEAKRLSTAFDSVTLYGEDPDPRPDIYGKVGNAGVSIATLDDLKVLYDGFDLTSPN 678
            +SEGM AKRLSTAFDSVTLYGE+PD RPDIYGKVGN+GVS+ATLDD+  LYDGFDL +P 
Sbjct: 653  LSEGMPAKRLSTAFDSVTLYGEEPDERPDIYGKVGNSGVSVATLDDMHALYDGFDLCAPQ 712

Query: 679  TSVSMTINGPAPTILAMFMNTALDQNLARFRADNGREPTEGEEAKIRAWVLQNVRGTVQA 738
            TSVSMTINGPAPTILAMF N A+DQ +AR     GR  +E E A+ R   L+NVRGTVQA
Sbjct: 713  TSVSMTINGPAPTILAMFFNVAIDQQIARQAQQLGRALSEDELAETRRMALENVRGTVQA 772

Query: 739  DILKEDQGQNTCIFSTAFSLKVMGDIQEYFVHHQVRNFYSVSISGYHIAEAGANPISQLA 798
            DILKEDQGQNTCIFST FSLKVMGDIQ YFV H+VRNFYSVSISGYHIAEAGANPISQLA
Sbjct: 773  DILKEDQGQNTCIFSTEFSLKVMGDIQAYFVEHRVRNFYSVSISGYHIAEAGANPISQLA 832

Query: 799  FTLANGFTYVEAYLARGMHIDDFAPNLSFFFSNGMDPEYSVLGRVARRIWAVTMRDKYGA 858
            +TLANGFTYVEAYLARGM IDDFAPNLSFFFSNGMDPEY+VLGRVARR+WA+ MR++YGA
Sbjct: 833  YTLANGFTYVEAYLARGMSIDDFAPNLSFFFSNGMDPEYTVLGRVARRVWAIAMRERYGA 892

Query: 859  NERSQKLKYHVQTSGRSLHAQEIAFNDIRTTLQALIAIYDNCNSLHTNAYDEAITTPTAE 918
            NERSQKLKYHVQTSGRSLHAQEI FNDIRTTLQALIAIYDNCNSLHTNA+DEAITTPT E
Sbjct: 893  NERSQKLKYHVQTSGRSLHAQEIDFNDIRTTLQALIAIYDNCNSLHTNAFDEAITTPTEE 952

Query: 919  SVRRALAIQLIINREWGLAKCENPNQGSFIIDELTDLVEAAVLREFERLAERGGVLGAME 978
            SVRRA+AIQLIINREWGLAK +NPNQGSF+IDELTDLVE AVL EF+RL ERGGVLGAME
Sbjct: 953  SVRRAVAIQLIINREWGLAKNQNPNQGSFVIDELTDLVEEAVLAEFDRLTERGGVLGAME 1012

Query: 979  TGYQRGRIQEESMLYEQRKHDGSLPIVGVNTFRNPEAGHAAPAHIELARSSEEEKQRQLA 1038
            TGYQRGRIQ+ESMLYE RKHDGS PIVGVNTF + +  H AP  I LARS+EEEKQ QL 
Sbjct: 1013 TGYQRGRIQDESMLYEHRKHDGSYPIVGVNTFVSAKP-HEAPTPIALARSTEEEKQSQLK 1071

Query: 1039 RLADFHARHAAEAPAMLQRLQRAVIDDQNVFAVLMDAVRVCSLGQITHALFEVGGQYRRN 1098
            RL DF ARH   APA L+RLQRAVIDD+NVFAVLMD VRVCSLGQITHALFEVGGQYRRN
Sbjct: 1072 RLRDFQARHRGAAPAALERLQRAVIDDENVFAVLMDVVRVCSLGQITHALFEVGGQYRRN 1131

Query: 1099 M 1099
            M
Sbjct: 1132 M 1132


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: 2995
Number of extensions: 115
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: 2
Length of query: 1099
Length of database: 1132
Length adjustment: 46
Effective length of query: 1053
Effective length of database: 1086
Effective search space:  1143558
Effective search space used:  1143558
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: 58 (26.9 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 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