GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mcmA in Dinoroseobacter shibae DFL-12

Align Methylmalonyl-CoA mutase; MCM; EC 5.4.99.2 (characterized)
to candidate 3607311 Dshi_0726 methylmalonyl-CoA mutase, large subunit (RefSeq)

Query= SwissProt::Q3J4D7
         (709 letters)



>FitnessBrowser__Dino:3607311
          Length = 712

 Score = 1201 bits (3107), Expect = 0.0
 Identities = 608/709 (85%), Positives = 652/709 (91%)

Query: 1   MTEDLDAWRKLAEKELKGKSPDSLTWNTLEGIPVKPLYTRADLAGMEHLDGLPGVAPFTR 60
           MT+  DAW  LA KEL+GK  ++LTW TLEGI VKPLYT  DL G++HL  +PG APFTR
Sbjct: 1   MTKGKDAWADLAAKELRGKPLETLTWKTLEGIDVKPLYTAEDLEGLDHLGSVPGQAPFTR 60

Query: 61  GVRATMYAGRPWTIRQYAGFSTAEASNAFYRKALAAGQQGVSVAFDLATHRGYDSDHPRV 120
           GV+ATMYAGRPWTIRQYAGFSTAE SNAFYRKALAAGQQGVSVAFDLATHRGYDSDHPRV
Sbjct: 61  GVKATMYAGRPWTIRQYAGFSTAEESNAFYRKALAAGQQGVSVAFDLATHRGYDSDHPRV 120

Query: 121 VGDVGKAGVAIDSIEDMKILFNGIPLEKISVSMTMNGAVIPILANFIVTGEEQGVPRAAL 180
            GDVGKAGVAIDS+EDMKILF+GIPL+++SVSMTMNGAVIPILANFIVTGEEQG  R+ L
Sbjct: 121 EGDVGKAGVAIDSVEDMKILFDGIPLDQVSVSMTMNGAVIPILANFIVTGEEQGHDRSVL 180

Query: 181 SGTIQNDILKEFMVRNTYIYPPEPSMRIIADIIEYTSKEMPKFNSISISGYHMQEAGANL 240
           SGTIQNDILKEFMVRNTY+YPPEPSMRIIADIIEYTS EMPKFNSISISGYHMQEAGANL
Sbjct: 181 SGTIQNDILKEFMVRNTYVYPPEPSMRIIADIIEYTSAEMPKFNSISISGYHMQEAGANL 240

Query: 241 VQELAYTLADGREYVRAALARGMNVDDFAGRLSFFFAIGMNFFMEAAKLRAARLLWHRIM 300
           VQELA+TLADGREYVRAA+ARGM+VD FAGRLSFFFAIGMNFFMEAAKLRAAR+LWH+IM
Sbjct: 241 VQELAFTLADGREYVRAAIARGMDVDKFAGRLSFFFAIGMNFFMEAAKLRAARMLWHKIM 300

Query: 301 SEFAPKKPGSLMLRTHCQTSGVSLQEQDPYNNVIRTAYEAMSAALGGTQSLHTNALDEAI 360
           SEF PK P S+MLRTHCQTSGVSLQEQDPYNNVIRTAYEAMSA LGGTQSLHTNALDEAI
Sbjct: 301 SEFEPKNPRSMMLRTHCQTSGVSLQEQDPYNNVIRTAYEAMSAVLGGTQSLHTNALDEAI 360

Query: 361 ALPTEFSARIARNTQIILQEETGVTRVVDPLAGSYYVESLTAELAEKAWALIEEVEAMGG 420
           ALPTEFSARIARNTQ+ILQEETGVT VVDPLAGSYYVESLT ELAEKAWALIEEVE +GG
Sbjct: 361 ALPTEFSARIARNTQLILQEETGVTNVVDPLAGSYYVESLTNELAEKAWALIEEVEELGG 420

Query: 421 MTKAVASGMPKLRIEESAARRQAAIDRGEDVIVGVNKYRLAKEDPIEILDIDNVAVRDAQ 480
           MTKAVASGMPKLRIEESAARRQA ID+G +VIVGVNKYR  KEDPI+IL+IDN  VRD Q
Sbjct: 421 MTKAVASGMPKLRIEESAARRQAMIDKGTEVIVGVNKYRKDKEDPIDILEIDNAKVRDGQ 480

Query: 481 IARLEKMRATRDEAACQAALDELTRRAAEGGNLLEAAVDASRARASVGEISMAMEKVFGR 540
           +ARL K+RA RDEAAC +AL E+ R AAEGGNLL AAV+A+RARASVGEISMAMEKVFGR
Sbjct: 481 VARLAKIRAERDEAACDSALAEVERCAAEGGNLLAAAVEAARARASVGEISMAMEKVFGR 540

Query: 541 HRAEVKTLSGVYGAAYEGDDGFAQIQRDVESFAEEEGRRPRMLVVKMGQDGHDRGAKVIA 600
           HRAEVKTL+GVYGAAYEGDDGFA IQ+ VE FA EEGRRPRMLVVKMGQDGHDRGAKVIA
Sbjct: 541 HRAEVKTLAGVYGAAYEGDDGFAAIQKSVEDFAAEEGRRPRMLVVKMGQDGHDRGAKVIA 600

Query: 601 TAFADIGFDVDVGTLFQTPEEAAQDAIDNDVHVVGISSLAAGHKTLAPKLIEALKEKGAG 660
           TAFADIGFDVDVG LFQTPEEAAQDAIDNDVHV+GISS AAGHKTLAPKL++ALK +GAG
Sbjct: 601 TAFADIGFDVDVGPLFQTPEEAAQDAIDNDVHVIGISSQAAGHKTLAPKLVDALKAQGAG 660

Query: 661 EILVICGGVIPQQDYDFLQQAGVKAIFGPGTNIPSAAKHILDLIREARS 709
           +ILVICGGVIPQQDY +L   GVKAIFGPGTNIP AA+ IL LIRE+R+
Sbjct: 661 DILVICGGVIPQQDYQYLYDRGVKAIFGPGTNIPEAAQDILRLIRESRA 709


Lambda     K      H
   0.318    0.133    0.377 

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: 1496
Number of extensions: 37
Number of successful extensions: 1
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: 709
Length of database: 712
Length adjustment: 39
Effective length of query: 670
Effective length of database: 673
Effective search space:   450910
Effective search space used:   450910
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 (21.7 bits)
S2: 55 (25.8 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