Alignments for a candidate for mcm-large in Nocardiopsis lucentensis DSM 44048

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcm-large in Nocardiopsis lucentensis DSM 44048

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_017600555.1 D471_RS0121620 methylmalonyl-CoA mutase

Query= BRENDA::P11653
         (728 letters)



>NCBI__GCF_000341125.1:WP_017600555.1
          Length = 740

 Score = 1005 bits (2599), Expect = 0.0
 Identities = 516/708 (72%), Positives = 581/708 (82%), Gaps = 6/708 (0%)

Query: 26  EELAAKAGTGEAWETAEQIPVGTLFNEDVYKDMDWLDTYAGIPPFVHGPYATMYAFRPWT 85
           +E   KA     WET E I V  L+       +D++    GIPP++ GPY TMY  +PWT
Sbjct: 28  QERGGKAVDALEWETPEGIAVKPLYTPADRAGLDFVGGLPGIPPYLRGPYPTMYVNQPWT 87

Query: 86  IRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPRVAGDVGMAGVAIDS 145
           IRQYAGFSTA+ SNAFYRRNLAAGQKGLSVAFDL THRGYDSD+PRVAGDVGMAGVAIDS
Sbjct: 88  IRQYAGFSTAEASNAFYRRNLAAGQKGLSVAFDLATHRGYDSDHPRVAGDVGMAGVAIDS 147

Query: 146 IYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLAGTIQNDILKEFM 205
           IYDMR+LF GIPLD+MSVSMTMNGAVLP+LALY+V AEEQGV PEQL+GTIQNDILKEFM
Sbjct: 148 IYDMRQLFDGIPLDRMSVSMTMNGAVLPVLALYIVAAEEQGVSPEQLSGTIQNDILKEFM 207

Query: 206 VRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISGYHMQEAGATADIEMAYTLADGVD 265
           VRNTYIYPP+PSMRIIS+IFAYTS  MP++NSISISGYHMQEAGATAD+E+AYTLADGV+
Sbjct: 208 VRNTYIYPPRPSMRIISDIFAYTSQRMPRFNSISISGYHMQEAGATADLELAYTLADGVE 267

Query: 266 YIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKLVHQFGPKNPKSMSL 325
           YIRAG+  GL+VD+FAPRLSFFW IGMNFFMEVAKLRAAR+LWA+LV   G    KS+SL
Sbjct: 268 YIRAGQRSGLDVDRFAPRLSFFWAIGMNFFMEVAKLRAARLLWARLVRDLGAVKDKSLSL 327

Query: 326 RTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHTQSLHTNSLDEAIALPTDFSARIARN 385
           RTHSQTSGWSLTAQDV+NNV RTC+EAMAATQGHTQSLHTN+LDEA+ALPTDFSARIARN
Sbjct: 328 RTHSQTSGWSLTAQDVFNNVARTCVEAMAATQGHTQSLHTNALDEALALPTDFSARIARN 387

Query: 386 TQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKAWGHIQEVEKVGGMAKAIEKGIPKMR 445
           TQL LQQESGTTRV+DPW GS YVE LT +LA KAW HIQEVEK GGMA AI+ G+PKMR
Sbjct: 388 TQLLLQQESGTTRVVDPWGGSYYVERLTQELAAKAWAHIQEVEKAGGMAAAIDAGLPKMR 447

Query: 446 IEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKLVKLRAERDP 505
           IEEAAARTQARIDSGRQP+IGVNKYR +    +DVLKVDN+ V A+Q  KL +LR ERD 
Sbjct: 448 IEEAAARTQARIDSGRQPVIGVNKYRPDTHDEIDVLKVDNAEVRAQQLDKLRRLREERDE 507

Query: 506 EKVKAALDKITWAAGNPD--DKDPDRNLLKLCIDAGRAMATVGEMSDALEKVFGRYTAQI 563
             V+AALD +T AAG     D+    NLL   +DA RA ATVGE+SDA+EKVF R++ QI
Sbjct: 508 TAVRAALDALTEAAGRESVADESLTNNLLAAAVDAARAKATVGEISDAMEKVFSRHSGQI 567

Query: 564 RTISGVYSKEVKNTPE----VEEARELVEEFEQAEGRRPRILLAKMGQDGHDRGQKVIAT 619
           RTI GVY  E   + +    +E     V+EF + EGRRPRIL+AKMGQDGHDRGQKVIAT
Sbjct: 568 RTIQGVYRDEAAGSGDAAGLMERVGARVDEFAETEGRRPRILVAKMGQDGHDRGQKVIAT 627

Query: 620 AYADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAGGHLTLVPALRKELDKLGRPD 679
           A+ADLGFDVDVGPLFQTP E A QAVEADVHVVGVSSLA GHLTLVPALR+EL KL R D
Sbjct: 628 AFADLGFDVDVGPLFQTPAEVAVQAVEADVHVVGVSSLAAGHLTLVPALREELAKLDRED 687

Query: 680 ILITVGGVIPEQDFDELRKDGAVEIYTPGTVIPESAISLVKKLRASLD 727
           I+I VGGVIP  DF+ LR+ GA  I+ PGTVI E+AI L+ +L   LD
Sbjct: 688 IMIVVGGVIPPADFEPLREMGASAIFPPGTVIAEAAIDLLDQLEERLD 735


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: 1531
Number of extensions: 55
Number of successful extensions: 3
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: 740
Length adjustment: 40
Effective length of query: 688
Effective length of database: 700
Effective search space:   481600
Effective search space used:   481600
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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