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

GapMind for catabolism of small carbon sources

Aligments 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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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