Aligments for a candidate for mcmA in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Aligments for a candidate for mcmA in Echinicola vietnamensis KMM 6221, DSM 17526

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate Echvi_2441 Echvi_2441 Methylmalonyl-CoA mutase, N-terminal domain/subunit

Query= BRENDA::Q8F222
         (1125 letters)



>FitnessBrowser__Cola:Echvi_2441
          Length = 1125

 Score = 1498 bits (3877), Expect = 0.0
 Identities = 754/1125 (67%), Positives = 901/1125 (80%), Gaps = 12/1125 (1%)

Query: 6    YTPKHKVRFITAASLFDGHDASINIMRRILQSSGVEVIHLGHNRSVREIVECAIQEDAQG 65
            Y PK  VR +TAASLFDGHDA+INIMRRI+QS G EVIHLGHNRSV+EIV CAIQED Q 
Sbjct: 8    YKPKSHVRIVTAASLFDGHDAAINIMRRIIQSVGCEVIHLGHNRSVQEIVSCAIQEDVQA 67

Query: 66   IAITSYQGGHVEYFKYMIDLLKEKGAGHIKVFGGGGGTILPSEIKELESYGVTRIYSPDD 125
            IAITSYQGGH+E+FKYM DLL+EKGAGHIK+FGGGGGTILP+EIKEL +YGV RIY+PDD
Sbjct: 68   IAITSYQGGHIEFFKYMYDLLQEKGAGHIKIFGGGGGTILPAEIKELHAYGVARIYAPDD 127

Query: 126  GRELGLQGMINDLIRRSDFIPPITFNGTLHSSLKD-KNPLAIAQMITLVENTFEREDLEK 184
            GR +GLQGMINDL+ ++DF      +G    +L D ++P  IA+ I+  EN  +      
Sbjct: 128  GRSMGLQGMINDLVGQADFPLGDKLDG---GALPDVRHPERIARWISAAENFPDAYQ--- 181

Query: 185  STLNEKLNFPPGTKSVPVLGITGTGGAGKSSLTDELVRRFLIDFPNKTIAILSVDPSKRK 244
             ++ EK       K+VPVLGITGTGGAGKSSL DEL RRFL+DFP+K +AI+SVDPSKRK
Sbjct: 182  -SMREKQGHGGEDKTVPVLGITGTGGAGKSSLVDELARRFLVDFPDKHLAIISVDPSKRK 240

Query: 245  TGGALLGDRIRMNSISHDRVYMRSFATREANIALNKNVKRSIEVLKSAGFDLIIVETAGI 304
            TGGALLGDRIRMN+I H RVYMRS ATR+AN++L+K+VK +++++K AGFDL+I+ET+GI
Sbjct: 241  TGGALLGDRIRMNAIHHPRVYMRSLATRQANLSLSKHVKDAVDIVKMAGFDLVILETSGI 300

Query: 305  GQSDSEITEVADVALYVMTPEYGAATQLEKIDMIDYADLIAINKFDKRGALDALRDVKKQ 364
            GQSD+E+ + AD++LYVMTPEYGAA+QLEKIDM+D+ADLIA+NKFDK+GA DALRDVKKQ
Sbjct: 301  GQSDTEVADHADLSLYVMTPEYGAASQLEKIDMLDFADLIALNKFDKKGAFDALRDVKKQ 360

Query: 365  FQRSRQLFDQNIDLMPVFGTIASQFNDPGTNLLYGNVIRFLSNKLNLDWSSSYEKEEGAS 424
            F R+  L+D   + +PV GTIASQFNDPG N LY  ++  L+     D++ S        
Sbjct: 361  FVRNHGLWDAKDEELPVIGTIASQFNDPGMNRLYRELMLRLTALKIADFTPSDGASLEEL 420

Query: 425  EKIFIIPPDRVRYLAEIREECGRYDQFTKNESDKARKLFQLSGAIEVLKSSGQDISI--- 481
            EK+FIIPP R RYLAEI EE  RY+Q+   + + A +L+ +  AIE  +   +  S    
Sbjct: 421  EKLFIIPPSRTRYLAEIVEENQRYEQWAATQKELANRLYGVKKAIETFEEEAEGESAVME 480

Query: 482  -LKLEYSKIENSLSLETKKILSSWEEKLKNYQGENFTYKVRDKEIKVSNTTVSLSNLKIP 540
             L+  Y+ + N L  E  + L +W+E + +Y  + FT+ VR KEI +   + SLS  +IP
Sbjct: 481  SLEAAYTALTNKLDAENLQWLENWKELVGSYANDQFTFMVRGKEIAIQTFSTSLSGTRIP 540

Query: 541  KVAVPKFKDWGEIVRWSFQENFPGEFPFTSGVFPFKRTGEDPTRMFAGEGGPERTNARFH 600
            KVA+PK++ WG++++W F+EN PG+FPFT+GVFPFKR GEDPTRMFAGEGGPERTN RFH
Sbjct: 541  KVALPKYEAWGDLLQWKFKENVPGKFPFTAGVFPFKREGEDPTRMFAGEGGPERTNRRFH 600

Query: 601  YVSLGMPAQRLSTAFDSVTLYGEDPGERPDIYGKIGNSGVSIATLDDAKKLYSGFDLCNP 660
            YVS  MPA+RLSTAFDSVTLYGEDPG RPDIYGKIGNSGV+I  LDD KKLY+GFDL +P
Sbjct: 601  YVSKDMPAKRLSTAFDSVTLYGEDPGYRPDIYGKIGNSGVNICCLDDMKKLYAGFDLADP 660

Query: 661  TTSVSMTINGPAPMVLAFFMNTAIDQACEKHILASGIEKSVRQKIESIYKEKKFPIPKYN 720
             TSVSMTINGPA  + AFFMNTAIDQ CE++I   G E  V  K++ +Y+E     P+Y 
Sbjct: 661  RTSVSMTINGPAATMTAFFMNTAIDQQCERYIYDKGSEGEVEAKLDEMYRENGLERPRYQ 720

Query: 721  TQIPEGNDGLGLMLLGVTGDEVLEKEVYEKIKQETLKLVRGTVQADILKEDQAQNTCIFS 780
              +PEGN+GLGL+LLGVTGD+VL KEVYE IK +TL  VRGTVQADILKEDQAQNTCIFS
Sbjct: 721  GTVPEGNNGLGLLLLGVTGDQVLPKEVYESIKADTLTKVRGTVQADILKEDQAQNTCIFS 780

Query: 781  TEFALKMMGDIQEFFIKNQVRNFYSVSISGYHIAEAGANPITQVAFTLANGLTYVEYFLS 840
            TEF+L++MGD+QE+FI   VRNFYSVSISGYHIAEAGANPITQ+A TL+NG TYVEY++S
Sbjct: 781  TEFSLRLMGDVQEYFIDQGVRNFYSVSISGYHIAEAGANPITQLALTLSNGFTYVEYYVS 840

Query: 841  RGMKIDDFAPNLSFFFSNGIDPEYAVIGRVARRIWAKAMKYKYGANDRSAMLKYHIQTSG 900
            RGM ++ FAPNLSFFFSNGIDPEYAVIGRVARRIWAKAMK KYGAN+RS MLKYHIQTSG
Sbjct: 841  RGMDVNAFAPNLSFFFSNGIDPEYAVIGRVARRIWAKAMKLKYGANERSQMLKYHIQTSG 900

Query: 901  RSLHAQEIAFNDIRTTLQALYAIYDNCNSLHTNAYDEAITTPTEESVRRAMAIQLIINRE 960
            RSLHAQEI FNDIRTTLQALYAIYDNCNSLHTNAYDEAITTPTE SVRRAMAIQLIIN+E
Sbjct: 901  RSLHAQEIDFNDIRTTLQALYAIYDNCNSLHTNAYDEAITTPTEASVRRAMAIQLIINKE 960

Query: 961  LGLSKNENPSQGSFIIEELTDLVEQAILEEFHKISERGGVLGAMEMMYQRNKIQEESLYY 1020
            LGL+KNENP QG+FIIEELTDLVE+A+  EF +I+ERGGVLGAME MYQR KIQEESL+Y
Sbjct: 961  LGLAKNENPLQGAFIIEELTDLVEEAVYAEFERITERGGVLGAMETMYQRGKIQEESLHY 1020

Query: 1021 ESLKHNGEFPVIGVNTFLSKEGSPTIVPQEVIRSTDEEKQAQISALREFHKRNEKDIENR 1080
            E+LKH G +P+IGVNTFLS  GSPTI P EVIR+T EEK+ QI  L   H++ E      
Sbjct: 1021 ETLKHAGTYPIIGVNTFLSSAGSPTITPGEVIRATQEEKEMQIKGLENLHRKYEFQSVEL 1080

Query: 1081 LRKLKSVSLSNGNIFQELMETSKKVSLGQMTHALYEVGGQYRRSM 1125
            L  LK  +++N N+F +LME  K  SLGQ+THALYEVGGQ+RR+M
Sbjct: 1081 LNDLKEAAVTNENLFSQLMEAVKCCSLGQITHALYEVGGQFRRNM 1125


Lambda     K      H
   0.317    0.135    0.379 

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: 3229
Number of extensions: 144
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: 1125
Length of database: 1125
Length adjustment: 46
Effective length of query: 1079
Effective length of database: 1079
Effective search space:  1164241
Effective search space used:  1164241
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 (21.6 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, 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