GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuB in Rhodobacter ovatus JA234

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_097031309.1 CRO07_RS14095 acetyl-CoA carboxylase biotin carboxylase subunit

Query= reanno::pseudo5_N2C3_1:AO356_01595
         (649 letters)



>NCBI__GCF_900207575.1:WP_097031309.1
          Length = 448

 Score =  415 bits (1066), Expect = e-120
 Identities = 215/443 (48%), Positives = 292/443 (65%), Gaps = 3/443 (0%)

Query: 9   LLVANRGEIACRVMRTARAMGLTTVAVHSATDRDARHSREADIRVDLGGSKAADSYLQID 68
           +L+ANRGEIA RV+R  R MG+ +VAVHS  D DA H R AD  V +G + + DSYL   
Sbjct: 5   ILIANRGEIALRVIRACREMGIKSVAVHSTADADAMHVRMADESVCIGPASSTDSYLSKA 64

Query: 69  KLIAAAKASGAQAIHPGYGFLSENAGFARAIENAGLIFLGPPASAIDAMGSKSAAKTLME 128
            +I+A + +GA+A+HPGYGFLSENA FA+A+++ G+ F+GP A  I  MG K  AK  M 
Sbjct: 65  AIISACEITGAEAVHPGYGFLSENAAFAQALQDHGIEFIGPTADHIRIMGDKITAKETMR 124

Query: 129 TAGVPLVPGYHGEAQDLETFRDAAERIGYPVLLKATAGGGGKGMKVVEDVSQLAEALASA 188
             GVP VPG  G   D E     A+ IG+PV++KATAGGGG+GMKV  +  +L  A  +A
Sbjct: 125 ALGVPCVPGSDGGVPDYEAAIGVAQSIGFPVIIKATAGGGGRGMKVARNAEELEVAFRTA 184

Query: 189 QREAQSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEEAPA 248
           + EA+++FG+  + +EKYL +PRH+EIQVF D  G  ++L ERDCS+QRRHQKV EEAP 
Sbjct: 185 RSEAKAAFGNDEVYMEKYLQRPRHIEIQVFGDGKGRAVHLGERDCSLQRRHQKVFEEAPG 244

Query: 249 PGLTPQLRRAMGEAAVRAAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPVTEAIT 308
           P +TP+LR  +G     A   I Y+GAGT+EFL +  GEF+F+EMNTRLQVEHPVTEAI 
Sbjct: 245 PVITPELRAKIGRICAEAVARINYIGAGTIEFLYE-DGEFYFIEMNTRLQVEHPVTEAIF 303

Query: 309 GLDLVAWQIRVAQGEPLPITQAQVPLLGHAIEVRLYAEDPGNDFLPATGRLALYRESAEG 368
           G+DLV  QIRVA G P+ + Q  + + GHAIEVR+ AE   N F P  G++ ++  +  G
Sbjct: 304 GVDLVREQIRVAAGLPMSLDQEALEINGHAIEVRINAEKLPN-FTPCPGKVRVF-HAPGG 361

Query: 369 PGRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFVIGGLKTNIGFLR 428
            G R+DS +  G  I P+YD ++GKLI  G DR +A  RL   L E ++ G+ T +    
Sbjct: 362 LGVRMDSALYGGYSIPPYYDSLIGKLIVHGRDRPEALARLHRALGELIVDGVDTTVPLFH 421

Query: 429 RIVAHPAFAAAELDTGFIPRYQA 451
            ++A P     + +  ++ ++ A
Sbjct: 422 ALLAEPDIQHGDYNIHWLEKWLA 444


Lambda     K      H
   0.319    0.134    0.390 

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: 723
Number of extensions: 27
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: 649
Length of database: 448
Length adjustment: 35
Effective length of query: 614
Effective length of database: 413
Effective search space:   253582
Effective search space used:   253582
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 2021. 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