GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuB in Paucidesulfovibrio gracilis DSM 16080

Align Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial; MCCase subunit alpha; 3-methylcrotonyl-CoA carboxylase 1; 3-methylcrotonyl-CoA carboxylase biotin-containing subunit; 3-methylcrotonyl-CoA:carbon dioxide ligase subunit alpha; EC 6.4.1.4 (characterized)
to candidate WP_268802025.1 B5D49_RS04650 biotin carboxylase N-terminal domain-containing protein

Query= SwissProt::Q96RQ3
         (725 letters)



>NCBI__GCF_900167125.1:WP_268802025.1
          Length = 470

 Score =  213 bits (543), Expect = 1e-59
 Identities = 165/471 (35%), Positives = 240/471 (50%), Gaps = 41/471 (8%)

Query: 48  NITKVLIANRGEIACRVMRTAKKLGVQTVAVYSEADRNSMHVDMADEAYSIGPAPSQQSY 107
           N  KVLIANRGEIA R+M     LG   VAVY+  D+ S HV+ A        A    SY
Sbjct: 2   NKHKVLIANRGEIAVRIMEACHDLGHDFVAVYTAEDQASGHVETARTLGGEHCAYRISSY 61

Query: 108 LSMEKIIQVAKTSAAQAIHPGCGFLSENMEFAE--LCKQEGIIFIGPPPSAIRDMGIKST 165
               +I  VA  + A AIHPG GF SEN  FA   + +Q  +IFIGP    IRD+G K  
Sbjct: 62  NDAGEIFSVADAAQATAIHPGYGFFSENYRFARRVVQRQRPMIFIGPSWWVIRDLGDKIN 121

Query: 166 SKSIMAAAGVPVVEG----YHGEDQSDQCLK-----EHARRIGYP-VMIKAVRGGGGKGM 215
           +K +  +  VP V G     + E ++++  +     + A+ I  P V++KA  GGGG G+
Sbjct: 122 TKRLARSLNVPTVPGSDRAIYDELEAEEIAENLFDFQEAQGISCPVVLVKASAGGGGMGI 181

Query: 216 RIVRSEQEFQEQLESARREAKKSFNDDAMLIEKFVDTPRHVEVQVFGDHHGNAVYLF-ER 274
             V     F++     R  + + FND+ +LIE+ V    H+EVQ+  +  G     F  R
Sbjct: 182 DEVPDMDRFRQIYRRIRNYSMRQFNDEGVLIEQRVFDFNHLEVQIVSERSGQRHVTFGTR 241

Query: 275 DCSVQR-RHQKIIEEAPA---PGI-----KSEVRKKLGEAAVRAAKAVNYVGAGTVEFIM 325
           +CSVQ    QK IE AP     GI       +V   + + ++R A+A+ Y   GT E+I+
Sbjct: 242 NCSVQSPGRQKRIETAPGFYPDGITYSFDAQKVLDDITDYSLRMAEAIKYDSVGTWEWIV 301

Query: 326 DSKHNFCFMEMNTRLQVEHPVTEMIT------GTDLVEWQLRIAAGEKIPLSQEEITLQG 379
             K +   +E+NTR+QVE+ V+  I       G +L+  Q+R+A G+ +  SQ++IT +G
Sbjct: 302 TPKGDPFLLEVNTRIQVENGVSAAIARIHGKDGVNLLREQIRLALGDPMGYSQKDITFEG 361

Query: 380 HAFEARIYAEDPSNNFMPVAGPLVHL---STPRADPSTRIETGVRQGDEVSVHYDPMIAK 436
            + E RI AED +N F P  G +      S P     T + T   +  ++   YDP +A 
Sbjct: 362 VSIEYRIIAEDTTNRFQPWVGQIDTFQWKSAPWLTMHTHVPTD--RAYQIPTEYDPNLAL 419

Query: 437 LVVWAADRQAALTKLRYSLRQYNIVG-------LHTNIDFL-LNLSGHPEF 479
            +VW AD + A  +   +L   ++ G       L +N+DFL  N  G  EF
Sbjct: 420 AIVWGADLEEAKARGMVALDGVDLQGNDTAGLELKSNLDFLRTNNKGLLEF 470


Lambda     K      H
   0.317    0.131    0.377 

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: 706
Number of extensions: 38
Number of successful extensions: 7
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: 725
Length of database: 470
Length adjustment: 36
Effective length of query: 689
Effective length of database: 434
Effective search space:   299026
Effective search space used:   299026
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: 53 (25.0 bits)

This GapMind analysis is from Apr 09 2024. 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