Alignments for a candidate for mcmA in Calditerrivibrio nitroreducens DSM 19672

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcmA in Calditerrivibrio nitroreducens DSM 19672

Align Methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_013450693.1 CALNI_RS02840 methylmalonyl-CoA mutase

Query= reanno::PS:Dsui_0519
         (721 letters)



>NCBI__GCF_000183405.1:WP_013450693.1
          Length = 716

 Score =  981 bits (2537), Expect = 0.0
 Identities = 479/704 (68%), Positives = 585/704 (83%), Gaps = 1/704 (0%)

Query: 19  WAKAAAKSAPGGDVNALNWITPEGLTVKPLYTKKDVEDLPY-ADTLPGFAPYLRGPQATM 77
           W   A K      ++ L W T EG  VKPLYT +D+++L +  DT PG  P++RGP ATM
Sbjct: 12  WEDKAKKEIKSDSLDKLIWHTAEGFDVKPLYTAEDLKNLTFDIDTYPGLPPFVRGPMATM 71

Query: 78  YAVRPWTIRQYAGFSTAEESNAFYRKALAAGGQGVSVAFDLATHRGYDSDNPRVLGDVGK 137
           YA +PWT+RQYAGFSTAEESNAFY++ LAAG QG+SVAFDLATHRGYDSD+PRV+GDVGK
Sbjct: 72  YAGKPWTVRQYAGFSTAEESNAFYKRNLAAGQQGLSVAFDLATHRGYDSDHPRVIGDVGK 131

Query: 138 AGVAIDSVEDMKILFDGIPLDKISVSMTMNGAVLPILAGYIVAAEEQGVSQEQLSGTIQN 197
           AGVAIDSVEDMKILFDGIPLDK+SVSMTMNGAV+P++A YIVAAEEQGVSQ++LSGTIQN
Sbjct: 132 AGVAIDSVEDMKILFDGIPLDKVSVSMTMNGAVIPVMAFYIVAAEEQGVSQDKLSGTIQN 191

Query: 198 DILKEFMVRNTYIYPPKPSMKIISDIFGYTAQHMPKFNSISISGYHIQEAGANQAIELAF 257
           DILKEFMVRNTYIYPP+PSM+I++DI  YT+++MPKFNSISISGYHIQEAGAN A+ELAF
Sbjct: 192 DILKEFMVRNTYIYPPEPSMRIVADIIEYTSKYMPKFNSISISGYHIQEAGANSALELAF 251

Query: 258 TLADGMEYVRTGIASGLDVDAFAGRLSFFWAVGMNFYLEIAKMRAGRMLWHRIMSQFNPK 317
           TLADG+EYVRT ++ GLD+D FA RLSFF+A+GMNF++EIAK+RA R LW +++SQFNPK
Sbjct: 252 TLADGLEYVRTALSRGLDIDKFAPRLSFFFAIGMNFFMEIAKLRAARYLWAKLISQFNPK 311

Query: 318 SAKSLMLRTHSQTSGWSLTEQDPYNNVVRTTIEAMAAVFGGTQSLHTNALDEAIALPTEF 377
             KS+ LRTH QTSGWSLT QDPYNNV+RTTIEA+AAV GGTQSLHTNALDEA+ALPT+F
Sbjct: 312 DPKSMALRTHCQTSGWSLTAQDPYNNVIRTTIEALAAVLGGTQSLHTNALDEALALPTDF 371

Query: 378 SARIARNTQLIIQEETHICNVVDPWAGSYMMEKLTQDMADKAWSIIQEIEAMGGMTKAVE 437
           SARIARNTQLIIQEET+ICNV+DP  GSY +E LT ++  +A  II E+EA+GGMTKA+E
Sbjct: 372 SARIARNTQLIIQEETNICNVIDPLGGSYYVENLTNELIKEAEKIIAEVEALGGMTKAIE 431

Query: 438 SGWAKMQVETCAADKQARIDSGKDVIVGVNKYKLAKEDQIDILDIDNHAVREAQIARLKK 497
           +G  K+++E  AA KQARIDSG DVIVGVNKYKL KED ID+L IDN AVR  QI +L +
Sbjct: 432 TGMPKLKIEESAAKKQARIDSGLDVIVGVNKYKLEKEDPIDVLMIDNTAVRNRQIQKLNE 491

Query: 498 IRASRDSAAVQAALDALTQCAESGEGNLLDLSVKAIRLRATVGEVSDALEKVFGRFRANN 557
           I+  RD+ AV+ AL+ +T+ A S + NLL+ +V A RLRAT+GE+SDA+E VFGR++A  
Sbjct: 492 IKGKRDNKAVKEALEKITEAARSNDKNLLEYAVNAARLRATLGEISDAMEAVFGRYKAEI 551

Query: 558 QTISGVYGGVVEGQESWESIKADIAKFAEEEGRRPRIMIAKLGQDGHDRGAKVVATAFAD 617
           +  +G YG     ++  E ++  + +F E EGRRPRI++ K+GQDGHDRG KVVATA AD
Sbjct: 552 RLQTGTYGNAYGKKDMIEEVRELVKEFEEVEGRRPRILMVKMGQDGHDRGVKVVATALAD 611

Query: 618 LGFDIDMGPLFQTPEEAARQAVENDVHAIGVSSLAAGHKTLLPALVNSLKEQGADDIIVF 677
           +GFD+D+GP+FQTPEEAA+ A+ENDVHA+GVS+LAAGH TL+PALV  LK+   DDI+VF
Sbjct: 612 MGFDVDVGPMFQTPEEAAKMAIENDVHAVGVSTLAAGHNTLVPALVEELKKNDGDDIVVF 671

Query: 678 AGGVIPAQDYDTLYAAGAKAIFGPGTRIEDSAKRVLEEIRKSRG 721
            GGVIP QDY+ LY +GA A+FGPGT I +SAK++LE IR  +G
Sbjct: 672 VGGVIPPQDYEFLYKSGASAVFGPGTNIVESAKKILECIRDRKG 715


Lambda     K      H
   0.317    0.132    0.380 

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: 1386
Number of extensions: 46
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: 721
Length of database: 716
Length adjustment: 40
Effective length of query: 681
Effective length of database: 676
Effective search space:   460356
Effective search space used:   460356
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: 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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Protein sequences (fasta format)
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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