Alignments for a candidate for mcm-large in Hydrogenophaga taeniospiralis NBRC 102512

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcm-large in Hydrogenophaga taeniospiralis NBRC 102512

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_068168315.1 HTA01S_RS06715 methylmalonyl-CoA mutase

Query= BRENDA::P11653
         (728 letters)



>NCBI__GCF_001592305.1:WP_068168315.1
          Length = 722

 Score =  828 bits (2139), Expect = 0.0
 Identities = 422/713 (59%), Positives = 535/713 (75%), Gaps = 7/713 (0%)

Query: 16  PVPADAARRFEELAAKAGTGEA--WETAEQIPVGTLFNEDVYKDMDWLDTYAGIPPFVHG 73
           P   +A  +  + +A  G   A  W T + I V  L+      ++ + +T  G  PF+ G
Sbjct: 12  PATLEAWTKAAQKSAPGGDVAALNWLTPDGISVKPLYTAADTANLPYTNTLPGFEPFIRG 71

Query: 74  PYATMYAFRPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPRVA 133
           P ATMYA RPWTIRQYAGFSTA+ESNAFYR+ LAAG +G+SVAFDL THRGYDSD+PRV 
Sbjct: 72  PQATMYAVRPWTIRQYAGFSTAEESNAFYRKALAAGGQGVSVAFDLATHRGYDSDHPRVT 131

Query: 134 GDVGMAGVAIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLA 193
           GDVG AGVAIDS+ DM+ LF  IPLD++SVSMTMNGAVLP+LA YV+ AEEQGV  ++L+
Sbjct: 132 GDVGKAGVAIDSVEDMKILFDQIPLDKVSVSMTMNGAVLPVLAGYVIAAEEQGVSQDKLS 191

Query: 194 GTIQNDILKEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISGYHMQEAGATAD 253
           GTIQNDILKEFMVRNTYIYPP+PSM+II +I  YT+ +MPK+NSISISGYHMQEAGA   
Sbjct: 192 GTIQNDILKEFMVRNTYIYPPEPSMKIIGDIIEYTAQHMPKFNSISISGYHMQEAGANQA 251

Query: 254 IEMAYTLADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKLVH 313
           +E+A+TLADG +Y++   + G++VD FA RLSFFW IGMNF++E+AK+RAAR+LW +++ 
Sbjct: 252 LELAFTLADGKEYVKTAIAKGMDVDGFAGRLSFFWAIGMNFYLEIAKMRAARLLWTRIMK 311

Query: 314 QFGPKNPKSMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHTQSLHTNSLDEAIA 373
            F  KNPKS+ LRTH QTSGWSLT QD YNNVVRT IEAMAA  G TQSLHTNS DEAIA
Sbjct: 312 GFDAKNPKSLMLRTHCQTSGWSLTEQDPYNNVVRTAIEAMAAVFGGTQSLHTNSFDEAIA 371

Query: 374 LPTDFSARIARNTQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKAWGHIQEVEKVGGM 433
           LPT+FSARIARNTQL +Q+E+  T V+DPW+GS  +E LT ++A KAW  I+EVE +GGM
Sbjct: 372 LPTEFSARIARNTQLIIQEETHITSVVDPWAGSYMMESLTQEMADKAWAIIEEVEAMGGM 431

Query: 434 AKAIEKGIPKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQK 493
            KA++ G  K++IE AAA  QARIDSG+  ++GVNKY+L+ E  ++   +DN  V   Q 
Sbjct: 432 TKAVDSGWAKLKIEAAAAEKQARIDSGKDVIVGVNKYKLKTEDAIEARDIDNVAVRDGQI 491

Query: 494 AKLVKLRAERDPEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAGRAMATVGEMSDALE 553
           A+L  +RA RD  KV+AAL+ +T AA     +    NLL L I A R  ATVGE+SDALE
Sbjct: 492 ARLKAIRASRDAGKVEAALNALTAAA-----ESGQGNLLDLSIQAMRLRATVGEVSDALE 546

Query: 554 KVFGRYTAQIRTISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPRILLAKMGQDGHDRG 613
           KVFGR+ A  + ++GVY+    +    +  +  + +F  A+GRRPR++++K+GQDGHDRG
Sbjct: 547 KVFGRHRADTQKVTGVYAAAYDSAEGWDALKGEINDFAVAQGRRPRVMISKLGQDGHDRG 606

Query: 614 QKVIATAYADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAGGHLTLVPALRKELD 673
            KV+ATA+ADLGFDVD+GPLFQTPEE ARQA+E DVH VGVS+LA GH TLVPA+  EL 
Sbjct: 607 AKVVATAFADLGFDVDMGPLFQTPEECARQAIENDVHAVGVSTLAAGHKTLVPAIIAELK 666

Query: 674 KLGRPDILITVGGVIPEQDFDELRKDGAVEIYTPGTVIPESAISLVKKLRASL 726
           K G  DI++ VGGVIP QD++ L + G   IY PGT IP SA  ++++++ +L
Sbjct: 667 KQGADDIIVFVGGVIPRQDYEMLYEAGVKGIYGPGTPIPASAKDVLEQIKKAL 719


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: 1396
Number of extensions: 50
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: 722
Length adjustment: 40
Effective length of query: 688
Effective length of database: 682
Effective search space:   469216
Effective search space used:   469216
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