GapMind for catabolism of small carbon sources

 

Alignments 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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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