GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuB in Brevibacterium jeotgali SJ5-8

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_101589300.1 BJEO58_RS09820 ATP-grasp domain-containing protein

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



>NCBI__GCF_900169175.1:WP_101589300.1
          Length = 600

 Score =  399 bits (1024), Expect = e-115
 Identities = 205/457 (44%), Positives = 286/457 (62%), Gaps = 10/457 (2%)

Query: 9   LLVANRGEIACRVMRTARAMGLTTVAVHSATDRDARHSREADIRVDLGGSKAADSYLQID 68
           +L+ANRGEIA R++R  R +G+ +VA ++A D DA     AD    L GS AA++YL I 
Sbjct: 23  VLIANRGEIALRIVRACRDLGIASVAAYTAADADALFVSLADDAYRLDGSGAAETYLSIP 82

Query: 69  KLIAAAKASGAQAIHPGYGFLSENAGFARAIENAGLIFLGPPASAIDAMGSKSAAKTLME 128
            ++  A  +GA A+HPGYG+L+E+  FA A+  AGL ++GP ASAIDA+G K+ A+ + +
Sbjct: 83  TMVELAHRAGADAVHPGYGYLAESGEFATAVAEAGLTWVGPTASAIDALGDKAGARAVAQ 142

Query: 129 TAGVPLVPGYHGEAQDLETFRDAAERIGYPVLLKATAGGGGKGMKVVEDVSQLAEALASA 188
             G P+  G  G  + +    D AE IGYPV +KA  GGGG+G +   D   L  A  +A
Sbjct: 143 AVGAPVPQGSAGPVESIPEALDVAEEIGYPVAIKAVHGGGGRGFRTAADAQALPAAFEAA 202

Query: 189 QREAQSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEEAPA 248
            REA+++FG    L+E+ +++PRHVE Q  AD HG  L ++ RDC++QRR+QKV+EEAPA
Sbjct: 203 SREAKAAFGRGDCLIEQQIIRPRHVETQCLADAHGRVLVVSTRDCTMQRRNQKVLEEAPA 262

Query: 249 PGLTPQLRRAMGEAAVRAAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPVTEAIT 308
           PGLT +    + +A+V   + +GYVGA T EFL+ A G   FME N R+QVEH +TE + 
Sbjct: 263 PGLTDEQEHLLEDASVNILRHVGYVGAATCEFLVGADGRITFMEANARIQVEHTITEEVA 322

Query: 309 GLDLVAWQIRVAQGEPLPITQAQVPLLGHAIEVRLYAEDPGNDFLPATGRLALYRESAEG 368
           G+DLVAWQ+R+A G  LP  ++     GHA + R+ AEDP + F+P  G +  YRE + G
Sbjct: 323 GVDLVAWQLRIAAGAALP--ESFPAPRGHAFQFRINAEDPTHGFVPVCGTITRYREPS-G 379

Query: 369 PGRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFVIGGLKTNIGFLR 428
           PG R+DSG+  G  +   +DPML KLI WG DRE A  R    +DEF + GL T +   R
Sbjct: 380 PGVRMDSGIATGTVVGTDFDPMLAKLIVWGPDRESALARSRRAIDEFALEGLPTLLPLHR 439

Query: 429 RIVAHPAFAAAE-------LDTGFIPRYQAQLLPEPS 458
            +     FA  E       L+  F+P + A+ LP+PS
Sbjct: 440 SLTDSAEFAGPELRVSTRWLEEDFMPAWSAERLPQPS 476


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: 958
Number of extensions: 46
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 649
Length of database: 600
Length adjustment: 37
Effective length of query: 612
Effective length of database: 563
Effective search space:   344556
Effective search space used:   344556
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: 54 (25.4 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