GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mcmA in Dyella japonica UNC79MFTsu3.2

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate N515DRAFT_0973 N515DRAFT_0973 methylmalonyl-CoA mutase

Query= BRENDA::Q8F222
         (1125 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0973
          Length = 1155

 Score = 1302 bits (3369), Expect = 0.0
 Identities = 675/1139 (59%), Positives = 850/1139 (74%), Gaps = 28/1139 (2%)

Query: 12   VRFITAASLFDGHDASINIMRRILQSSGVEVIHLGHNRSVREIVECAIQEDAQGIAITSY 71
            +RF+TAASLFDGHDA+INIMRRI+QS G EVIHLGHNRSV ++V  A+QEDA  IA++SY
Sbjct: 20   LRFVTAASLFDGHDAAINIMRRIIQSQGAEVIHLGHNRSVEDVVRAALQEDADAIALSSY 79

Query: 72   QGGHVEYFKYMIDLLKEKGAGHIKVFGGGGGTILPSEIKELESYGVTRIYSPDDGRELGL 131
            QGGHVEYFKYM+D+LKE GA HI+VFGGGGGTI P EI+EL++YGV RIY P+DG +LGL
Sbjct: 80   QGGHVEYFKYMVDMLKEHGAAHIRVFGGGGGTITPEEIRELQAYGVERIYHPNDGMKLGL 139

Query: 132  QGMINDLIRRSDFIPPITFNGTLHSSLKDKNPLAIAQMITLVENTFEREDLEKSTLNE-K 190
              MI D++RR+             +++  +  +     I  + ++ E   L ++ L+  +
Sbjct: 140  TEMIEDVMRRTREAADQRAGAEQATAVAPRVDIDDEISIGHMLSSIEEGQLPEAELDHLR 199

Query: 191  LNFPPGTKSVPVLGITGTGGAGKSSLTDELVRRFLIDFPNKTIAILSVDPSKRKTGGALL 250
              +    K  PVLG+TGTGGAGKSS+ DEL+ RFL  FP+  IA+L+VDP++R++GGALL
Sbjct: 200  KQWKMAGKQTPVLGVTGTGGAGKSSVVDELLLRFLHAFPDMRIAVLAVDPTRRRSGGALL 259

Query: 251  GDRIRMNSISHDRVYMRSFATREANIALNKNVKRSIEVLKSAGFDLIIVETAGIGQSDSE 310
            GDRIRMNS+   RVYMRS ATR  + A +  +   I+ LK+  +DL+IVETAGIGQSDSE
Sbjct: 260  GDRIRMNSLRSHRVYMRSMATRRQHAATSVVLHDCIDFLKAQPYDLVIVETAGIGQSDSE 319

Query: 311  ITEVADVALYVMTPEYGAATQLEKIDMIDYADLIAINKFDKRGALDALRDVKKQFQRSRQ 370
            I ++ D  +YVMT +YGAA+QLEKIDM+D+A+L+ +NKFDKRGA DALRDV+KQ++R+R 
Sbjct: 320  IVDLVDFPMYVMTSDYGAASQLEKIDMLDFAELVVLNKFDKRGAEDALRDVRKQWKRNRT 379

Query: 371  LFDQNIDLMPVFGTIASQFNDPGTNLLYGNVIRFLSNKLNLD---WSSSYEKEEGASEKI 427
             F    D +PV+ TIASQFNDPG   ++ N+ R L +KL L    W+   +         
Sbjct: 380  AFALKDDEVPVYPTIASQFNDPGVTWMFANLCRLLRDKLTLPAPKWTPELDTSLKEPRAT 439

Query: 428  FIIPPDRVRYLAEIREECGRYDQFTKNESDKARK-------LFQLSGA----------IE 470
             +IP  RVRYLAEI E+    +   + E++ A K       L  L  A           +
Sbjct: 440  VLIPGSRVRYLAEIAEQGRGINAGIEREAEFASKAQHYYESLKDLGDARLPRELARYDSQ 499

Query: 471  VLKSSGQDISILKLE--YSKIENSLSLETKKILSSWEEKLKNYQGENFTYKVRDKEIKVS 528
             L   G D ++L L   Y++    LS E   +L  W  + K+   E   YKVRDK I+V 
Sbjct: 500  SLHEEGADRTLLTLRQRYNQAVKELSHEAVHLLHDWPARYKSVTDEYNEYKVRDKTIRVE 559

Query: 529  NTTVSLSNLKIPKVAVPKFKDWGEIVRWSFQENFPGEFPFTSGVFPFKRTGEDPTRMFAG 588
            N   SLS+ KIPKV+ P+ KDWG++VR+  +EN PG +P+T GV+P++RTGEDPTRMFAG
Sbjct: 560  NYRESLSHQKIPKVSPPRTKDWGDLVRFLMRENLPGYYPYTGGVYPYRRTGEDPTRMFAG 619

Query: 589  EGGPERTNARFHYVSLGMPAQRLSTAFDSVTLYGEDPGERPDIYGKIGNSGVSIATLDDA 648
            EG PERTN RFHY+S G  A RLSTAFDSVTLYGEDP  RPDIYGKIGNSGV++ATLDD 
Sbjct: 620  EGTPERTNRRFHYLSQGGAATRLSTAFDSVTLYGEDPAPRPDIYGKIGNSGVNVATLDDM 679

Query: 649  KKLYSGFDLCNPTTSVSMTINGPAPMVLAFFMNTAIDQACEKHILASGIE-KSVRQKIES 707
            KKLYSGFDL  P++SVSMTINGPAP++LA FMNTAIDQ  EKH+ A        +QKI +
Sbjct: 680  KKLYSGFDLSAPSSSVSMTINGPAPIILAMFMNTAIDQNIEKHLKADPARWAEAQQKIAA 739

Query: 708  IYKEKKFPIPKYNTQIPEGNDGLGLMLLGVTGDEVLEKEVYEKIKQETLKLVRGTVQADI 767
            +        P+Y+ ++P+GN+GLGL LLG+TGD++++ + Y +IK+ETL++VRGTVQADI
Sbjct: 740  LQSHGG---PRYSGELPKGNEGLGLGLLGITGDQLVDAQTYARIKEETLQIVRGTVQADI 796

Query: 768  LKEDQAQNTCIFSTEFALKMMGDIQEFFIKNQVRNFYSVSISGYHIAEAGANPITQVAFT 827
            LKEDQAQNTCIFSTEFAL+MMGDIQ++F+ ++VRNFYSVSISGYHIAEAGANPI+Q+AFT
Sbjct: 797  LKEDQAQNTCIFSTEFALRMMGDIQQYFVDHKVRNFYSVSISGYHIAEAGANPISQLAFT 856

Query: 828  LANGLTYVEYFLSRGMKIDDFAPNLSFFFSNGIDPEYAVIGRVARRIWAKAMKYKYGAND 887
            L+NG T VEY+L+RGM IDDFAPNLSFFFSNG+DPEY VIGRVARRIWA+AM+ +YGA+ 
Sbjct: 857  LSNGFTIVEYYLARGMHIDDFAPNLSFFFSNGMDPEYTVIGRVARRIWARAMRERYGASA 916

Query: 888  RSAMLKYHIQTSGRSLHAQEIAFNDIRTTLQALYAIYDNCNSLHTNAYDEAITTPTEESV 947
            RS MLKYHIQTSGRSLHAQEI FNDIRTTLQALYA++DNCNSLHTNAYDEAITTPTEESV
Sbjct: 917  RSQMLKYHIQTSGRSLHAQEIQFNDIRTTLQALYALFDNCNSLHTNAYDEAITTPTEESV 976

Query: 948  RRAMAIQLIINRELGLSKNENPSQGSFIIEELTDLVEQAILEEFHKISERGGVLGAMEMM 1007
            RRA+AIQLIINRELGL+ NENP QGSF+++ LTDLVE+A+  EF  ISERGGVLGAM+ M
Sbjct: 977  RRAVAIQLIINRELGLNFNENPWQGSFVVDALTDLVEEAVYREFEAISERGGVLGAMDTM 1036

Query: 1008 YQRNKIQEESLYYESLKHNGEFPVIGVNTFLSKEGSPTIVPQ-EVIRSTDEEKQAQISAL 1066
            YQR KIQEES+YYE  KH+G  P+IGVNTFL K+    I  + E+IRST+EEK  QI  +
Sbjct: 1037 YQRGKIQEESMYYEQKKHDGSLPLIGVNTFLPKDHGGEIATEIELIRSTEEEKGQQIDNV 1096

Query: 1067 REFHKRNEKDIENRLRKLKSVSLSNGNIFQELMETSKKVSLGQMTHALYEVGGQYRRSM 1125
            + + K         L+ L++ +    N+F++LME  K  SLGQ++HALY+VGG+YRR+M
Sbjct: 1097 QAYAKARNGLAPESLKILQNTARERRNVFEQLMEAVKYNSLGQISHALYDVGGEYRRNM 1155


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: 3030
Number of extensions: 135
Number of successful extensions: 7
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: 1155
Length adjustment: 46
Effective length of query: 1079
Effective length of database: 1109
Effective search space:  1196611
Effective search space used:  1196611
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