Alignments for a candidate for mcmA in Pedobacter sp. GW460-11-11-14-LB5

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcmA in Pedobacter sp. GW460-11-11-14-LB5

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate CA265_RS14780 CA265_RS14780 methylmalonyl-CoA mutase

Query= BRENDA::Q8F222
         (1125 letters)



>FitnessBrowser__Pedo557:CA265_RS14780
          Length = 1129

 Score = 1544 bits (3997), Expect = 0.0
 Identities = 773/1135 (68%), Positives = 929/1135 (81%), Gaps = 19/1135 (1%)

Query: 2    ETQIYTPKHKVRFITAASLFDGHDASINIMRRILQSSGVEVIHLGHNRSVREIVECAIQE 61
            + +IY PK+K+RF+TAASLFDGHDA+INIMRRILQSSG EVIHLGHNRSV E+V CAIQE
Sbjct: 3    QVEIYKPKNKIRFVTAASLFDGHDATINIMRRILQSSGAEVIHLGHNRSVDEVVNCAIQE 62

Query: 62   DAQGIAITSYQGGHVEYFKYMIDLLKEKGAGHIKVFGGGGGTILPSEIKELESYGVTRIY 121
            D QGIA+TSYQGGH+EYFKYM DLL+E+G+GHIK+F GGGG ILPSEI+EL++YG+++IY
Sbjct: 63   DVQGIAMTSYQGGHIEYFKYMYDLLQERGSGHIKIFAGGGGVILPSEIEELQAYGISKIY 122

Query: 122  SPDDGRELGLQGMINDLIRRSDFIPPITFNGTLHSSLKDKNPLAIAQMITLVENTFERED 181
            SPDDGR++GLQGMIND++ ++DFI   +    L + +  K+  AIA  IT+ EN  + E 
Sbjct: 123  SPDDGRKMGLQGMINDMLVQTDFITKASITNELET-IPSKDIKAIAGAITVAEN--DPEG 179

Query: 182  LEKSTLNEKLNFPPGTKSVPVLGITGTGGAGKSSLTDELVRRFLIDFPNKTIAILSVDPS 241
             +K    ++L       + P+LGITGTGGAGKSSL DELVRRFL++  +KT+AI+SVDPS
Sbjct: 180  AQKFV--DELKKLSKNNTAPILGITGTGGAGKSSLVDELVRRFLVEVKDKTLAIISVDPS 237

Query: 242  KRKTGGALLGDRIRMNSISHDRVYMRSFATREANIALNKNVKRSIEVLKSAGFDLIIVET 301
            KRKTGGALLGDRIRMN+I++ RVYMRS ATR+AN+AL+KNV+ SI++ K+AG+DLIIVET
Sbjct: 238  KRKTGGALLGDRIRMNAINNPRVYMRSLATRQANLALSKNVQESIDICKAAGYDLIIVET 297

Query: 302  AGIGQSDSEITEVADVALYVMTPEYGAATQLEKIDMIDYADLIAINKFDKRGALDALRDV 361
            +GIGQSD+EITE  DV+LYVMTPE+GAATQLEKIDM+D+ADL+AINKFDKRGALDALRDV
Sbjct: 298  SGIGQSDTEITEHCDVSLYVMTPEFGAATQLEKIDMLDFADLVAINKFDKRGALDALRDV 357

Query: 362  KKQFQRSRQLFDQNIDLMPVFGTIASQFNDPGTNLLYGNVIRFLSNKLNLDWSSSYEKEE 421
            +KQ++R+  +FD   D +PV+GT+ASQFNDPG N L+  ++  +  K   D+ +  E   
Sbjct: 358  RKQYKRNHNIFDAKDDEIPVYGTMASQFNDPGMNNLFVALMEQIKVKTGTDFKAKMELTS 417

Query: 422  GASEKIFIIPPDRVRYLAEIREECGRYDQFTKNESDKARKLFQLSGAIEVLKSS------ 475
              SEKI+IIPPDR+RYLAEI E    Y+++   ++  ARK++QL G I++L  +      
Sbjct: 418  DQSEKIYIIPPDRIRYLAEIAEASQMYNEWVDKQATIARKMYQLKGVIDLLSEANLPDKS 477

Query: 476  -----GQDISILKLEYSKIENSLSLETKKILSSWEEKLKNYQGENFTYKVRDKEIKVSNT 530
                 G D+  +   Y+  E  L  E K++L  W +  + Y+ E F YKVRDKEIK    
Sbjct: 478  KVSPTGGDLEGV---YAFFEEQLDGECKRLLRQWPDTKRAYKEEFFIYKVRDKEIKQPLF 534

Query: 531  TVSLSNLKIPKVAVPKFKDWGEIVRWSFQENFPGEFPFTSGVFPFKRTGEDPTRMFAGEG 590
              SLS L IPKV++P+++DWG+I+RW   EN PGEFP+ +GVFP KR GEDPTRMFAGEG
Sbjct: 535  YESLSKLNIPKVSLPRYEDWGDILRWLLTENLPGEFPYAAGVFPLKREGEDPTRMFAGEG 594

Query: 591  GPERTNARFHYVSLGMPAQRLSTAFDSVTLYGEDPGERPDIYGKIGNSGVSIATLDDAKK 650
            GPERTN RFHYVSLG PA RLSTAFDSVTLYGEDP  RPDIYGKIGNSGV IATLDDAKK
Sbjct: 595  GPERTNKRFHYVSLGQPAHRLSTAFDSVTLYGEDPHIRPDIYGKIGNSGVCIATLDDAKK 654

Query: 651  LYSGFDLCNPTTSVSMTINGPAPMVLAFFMNTAIDQACEKHILASGIEKSVRQKIESIYK 710
            LYSGFDLC P+TSVSMTINGPAPM+L FFMN AIDQ CEK+I+ + + K V  KI++IY+
Sbjct: 655  LYSGFDLCAPSTSVSMTINGPAPMLLGFFMNAAIDQQCEKYIIENDLTKEVEAKIDAIYQ 714

Query: 711  EKKFPIPKYNTQIPEGNDGLGLMLLGVTGDEVLEKEVYEKIKQETLKLVRGTVQADILKE 770
             K  P P YN  +PEGNDGLGLMLLGVTGD+VL  ++Y KI+ + +  VRGTVQADILKE
Sbjct: 715  AKNIPRPSYNGTLPEGNDGLGLMLLGVTGDQVLPADIYAKIRTKAISSVRGTVQADILKE 774

Query: 771  DQAQNTCIFSTEFALKMMGDIQEFFIKNQVRNFYSVSISGYHIAEAGANPITQVAFTLAN 830
            DQAQNTCIFSTEFAL+MMGDIQ++FI  +VRNFYSVSISGYHIAEAGANPI+Q+AFTL+N
Sbjct: 775  DQAQNTCIFSTEFALRMMGDIQKYFIDEKVRNFYSVSISGYHIAEAGANPISQLAFTLSN 834

Query: 831  GLTYVEYFLSRGMKIDDFAPNLSFFFSNGIDPEYAVIGRVARRIWAKAMKYKYGANDRSA 890
            G T+VEY+LSRGM IDDFAPNLSFFFSNGIDPEYAVIGRVARRIWAKA+K KY  NDRS 
Sbjct: 835  GFTFVEYYLSRGMHIDDFAPNLSFFFSNGIDPEYAVIGRVARRIWAKAIKNKYKGNDRSQ 894

Query: 891  MLKYHIQTSGRSLHAQEIAFNDIRTTLQALYAIYDNCNSLHTNAYDEAITTPTEESVRRA 950
             LKYHIQTSGRSLHAQEI FNDIRTTLQALYAIYDNCNSLHTNAYDEAITTPTEESVRRA
Sbjct: 895  KLKYHIQTSGRSLHAQEIDFNDIRTTLQALYAIYDNCNSLHTNAYDEAITTPTEESVRRA 954

Query: 951  MAIQLIINRELGLSKNENPSQGSFIIEELTDLVEQAILEEFHKISERGGVLGAMEMMYQR 1010
            MAIQLIINRELGL+KNENP QG+FIIEELTDLVE A+L EF +I++RGGVLGAME MYQR
Sbjct: 955  MAIQLIINRELGLAKNENPLQGAFIIEELTDLVEDAVLAEFKRINDRGGVLGAMETMYQR 1014

Query: 1011 NKIQEESLYYESLKHNGEFPVIGVNTFLSKEGSPTIVPQEVIRSTDEEKQAQISALREFH 1070
             KIQEESLYYE+LKH GE+P++GVNTFL+K GSPTIVP EVIR+T++EKQ QISAL++F 
Sbjct: 1015 GKIQEESLYYETLKHTGEYPIVGVNTFLNKNGSPTIVPGEVIRATEDEKQYQISALQKFQ 1074

Query: 1071 KRNEKDIENRLRKLKSVSLSNGNIFQELMETSKKVSLGQMTHALYEVGGQYRRSM 1125
             RN     + L++L+  +++  NIF++LME  K  SLGQ++ ALYEVGGQYRR+M
Sbjct: 1075 DRNADRAVDLLKQLQKSAIAGDNIFEQLMEVCKICSLGQISKALYEVGGQYRRNM 1129


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: 3257
Number of extensions: 133
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: 1129
Length adjustment: 46
Effective length of query: 1079
Effective length of database: 1083
Effective search space:  1168557
Effective search space used:  1168557
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
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