GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mcmA in Haloterrigena daqingensis JX313

Align Methylmalonyl-CoA mutase; MCM; EC 5.4.99.2 (characterized)
to candidate WP_076581961.1 BB347_RS05900 methylmalonyl-CoA mutase family protein

Query= SwissProt::P27253
         (714 letters)



>NCBI__GCF_001971705.1:WP_076581961.1
          Length = 560

 Score =  504 bits (1299), Expect = e-147
 Identities = 268/514 (52%), Positives = 347/514 (67%), Gaps = 4/514 (0%)

Query: 32  GIAIKPLYTEADLDNLEVTGTL--PGLPPYVRGPRATMYTAQPWTIRQYAGFSTAKESNA 89
           G  +  LYT AD+ +++    L  PG PPY RG  +T Y  + WT+RQYAGFST +++N 
Sbjct: 42  GQTVDRLYTPADISDVDYQEDLGYPGEPPYTRGVYSTGYRGRLWTMRQYAGFSTPEDTNE 101

Query: 90  FYRRNLAAGQKGLSVAFDLATHRGYDSDNPRVAGDVGKAGVAIDTVEDMKVLFDQIPLDK 149
            Y   L  GQ GLS+AFDL T  G+DSD    AG++GKAGVAID++ DM+ +FD IPLD+
Sbjct: 102 RYHYLLDQGQTGLSMAFDLPTQMGHDSDASMSAGEIGKAGVAIDSLADMETVFDGIPLDE 161

Query: 150 MSVSMTMNGAVLPVLAFYIVAAEEQGVTPDKLTGTIQNDILKEYLCRNTYIYPPKPSMRI 209
           +S SMT+N     +LA YI   ++QGV  ++L GTIQNDILKEY+ RNTYIYPP+ SMRI
Sbjct: 162 VSTSMTINAPASVLLAMYIAVGDQQGVDREQLRGTIQNDILKEYIARNTYIYPPESSMRI 221

Query: 210 IADIIAWCSGNMPRFNTISISGYHMGEAGANCVQQVAFTLADGIEYIKAAISAGLKIDDF 269
           I DI  +C+   P+FNTISISGYH+ EAG+   Q++AFTL DGIEY++ AI AGL +DDF
Sbjct: 222 ITDIFEFCASETPKFNTISISGYHIREAGSTAAQELAFTLGDGIEYVETAIEAGLDVDDF 281

Query: 270 APRLSFFFGIGMDLFMNVAMLRAARYLWSEAV-SGFGAQDPKSLALRTHCQTSGWSLTEQ 328
           AP+LSFFF    ++F  VA  RAAR +W + +   F A DPKS  L+ H QT+G  LT Q
Sbjct: 282 APQLSFFFNGHNNIFEEVAKFRAARRMWHDIIDERFDANDPKSKQLKFHTQTAGSMLTAQ 341

Query: 329 DPYNNVIRTTIEALAATLGGTQSLHTNAFDEALGLPTDFSARIARNTQIIIQEESELCRT 388
              NNV+R   +ALAA LGGTQSLHTN  DEAL LPT+ S R A  TQ I+  ES    T
Sbjct: 342 QIENNVVRVAYQALAAVLGGTQSLHTNGKDEALALPTEESVRTALRTQQILAHESGAADT 401

Query: 389 VDPLAGSYYIESLTDQIVKQARAIIQQIDEAGGMAKAIEAGLPKRMIEEASAREQSLIDQ 448
           +DPLAGSYY+ESLTD + ++A  I++++DE GGM +AIE    +R I++ S   Q  ID 
Sbjct: 402 IDPLAGSYYVESLTDDVEEEAYEILEEVDERGGMREAIEQQWVQRQIQDTSFDRQKEIDS 461

Query: 449 GKRVIVGVNKYKLDHEDETDVLEIDNVMVRNEQIASLERIRATRDDAAVTAALNALTHAA 508
             R+IVGVN++++D + E DV EI     +  QI SLE  RA RDD AV A L+AL  AA
Sbjct: 462 NDRIIVGVNEFEVDEDPEMDVQEITE-EDQQRQIDSLESTRADRDDDAVEAKLDALREAA 520

Query: 509 QHNENLLAAAVNAARVRATLGEISDALEVAFDRY 542
           Q  +NL+   ++A +V AT+GEI + L   F  Y
Sbjct: 521 QGEDNLMPYIIDAVKVYATVGEICNVLRDEFGEY 554


Lambda     K      H
   0.318    0.133    0.381 

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: 991
Number of extensions: 44
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: 714
Length of database: 560
Length adjustment: 38
Effective length of query: 676
Effective length of database: 522
Effective search space:   352872
Effective search space used:   352872
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: 54 (25.4 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

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:

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