GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mcm-large in Rhodobacter ovatus JA234

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_097028688.1 CRO07_RS00240 methylmalonyl-CoA mutase

Query= BRENDA::P11653
         (728 letters)



>NCBI__GCF_900207575.1:WP_097028688.1
          Length = 709

 Score =  832 bits (2148), Expect = 0.0
 Identities = 428/702 (60%), Positives = 526/702 (74%), Gaps = 9/702 (1%)

Query: 26  EELAAKAGTGEAWETAEQIPVGTLFNEDVYKDMDWLDTYAGIPPFVHGPYATMYAFRPWT 85
           +EL  ++     W T E IPV  L+     + +D LD   G+ PF  G  ATMYA RPWT
Sbjct: 14  KELKGRSPDSLTWNTLEGIPVKPLYTRADIEGLDHLDGVPGVAPFTRGVRATMYAGRPWT 73

Query: 86  IRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPRVAGDVGMAGVAIDS 145
           IRQYAGFSTA+ SNAFYR+ LAAGQ+G+SVAFDL THRGYDSD+PRV GDVG AGVAIDS
Sbjct: 74  IRQYAGFSTAEASNAFYRKALAAGQQGVSVAFDLATHRGYDSDHPRVVGDVGKAGVAIDS 133

Query: 146 IYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLAGTIQNDILKEFM 205
           + DM+ LF GIPL+++SVSMTMNGAV+PILA ++VT EEQGV   +L+GTIQNDILKEFM
Sbjct: 134 VEDMKILFDGIPLEKISVSMTMNGAVIPILASFIVTGEEQGVPRAELSGTIQNDILKEFM 193

Query: 206 VRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISGYHMQEAGATADIEMAYTLADGVD 265
           VRNTYIYPP+PSMRII++I  YT+  MPK+NSISISGYHMQEAGA    E+AYTLADG +
Sbjct: 194 VRNTYIYPPEPSMRIIADIIEYTAKEMPKFNSISISGYHMQEAGANLVQELAYTLADGRE 253

Query: 266 YIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKLVHQFGPKNPKSMSL 325
           Y+RA  + G+NVD+FA RLSFF+ IGMNFFME AKLRAARMLW +++ +F PK P S+ L
Sbjct: 254 YVRAAIARGMNVDEFAGRLSFFFAIGMNFFMEAAKLRAARMLWHRIMSEFEPKKPGSLML 313

Query: 326 RTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHTQSLHTNSLDEAIALPTDFSARIARN 385
           RTH QTSG SL  QD YNNV+RT  EA+AA  G TQSLHTN+LDEAIALPT+FSARIARN
Sbjct: 314 RTHCQTSGVSLQEQDPYNNVIRTAYEALAAALGGTQSLHTNALDEAIALPTEFSARIARN 373

Query: 386 TQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKAWGHIQEVEKVGGMAKAIEKGIPKMR 445
           TQL LQ+E+G T+V+DP +GS YVE LT +LA KAW  I+EVE +GGM KA+  G+PK+R
Sbjct: 374 TQLILQEETGVTKVVDPLAGSYYVESLTNELAEKAWALIEEVEAMGGMTKAVASGMPKLR 433

Query: 446 IEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKLVKLRAERDP 505
           IEE+AAR QA ID G   ++GVNKYRL  E P+++L +DN  V   Q A+L K+RA RD 
Sbjct: 434 IEESAARRQAAIDRGEDVIVGVNKYRLAKEDPIEILDIDNVAVRDAQIARLEKMRATRDE 493

Query: 506 EKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAGRAMATVGEMSDALEKVFGRYTAQIRT 565
              + ALD++T  A          NLL+  +DA RA A+VGE+S A+EKVFGR+ A+++T
Sbjct: 494 AACQKALDELTRRASE------GGNLLEAAVDASRARASVGEISMAMEKVFGRHRAEVKT 547

Query: 566 ISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPRILLAKMGQDGHDRGQKVIATAYADLG 625
           +SGVY    +        ++ VE F + EGRRPR+L+ KMGQDGHDRG KVIATA+AD+G
Sbjct: 548 LSGVYGAAYEGDDGFAAIQKDVETFAEEEGRRPRMLVVKMGQDGHDRGAKVIATAFADIG 607

Query: 626 FDVDVGPLFQTPEETARQAVEADVHVVGVSSLAGGHLTLVPALRKELDKLGRPDILITVG 685
           FDVDVG LFQTPEE A+ A++ DVHVVG+SSLA GH TL P L + L   G  DIL+  G
Sbjct: 608 FDVDVGTLFQTPEEAAQDAIDNDVHVVGISSLAAGHKTLAPKLIEALKAQGAGDILVICG 667

Query: 686 GVIPEQDFDELRKDGAVEIYTPGTVIPESA---ISLVKKLRA 724
           GVIP+QD+D L   G   I+ PGT IP +A   + L+++ RA
Sbjct: 668 GVIPQQDYDFLYNSGVKAIFGPGTNIPSAAKQILDLIRQARA 709


Lambda     K      H
   0.317    0.133    0.389 

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: 1316
Number of extensions: 41
Number of successful extensions: 2
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: 728
Length of database: 709
Length adjustment: 40
Effective length of query: 688
Effective length of database: 669
Effective search space:   460272
Effective search space used:   460272
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 24 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