GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagB in Megamonas funiformis YIT 11815

Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_008538534.1 HMPREF9454_RS05935 glutamine--fructose-6-phosphate transaminase (isomerizing)

Query= reanno::Caulo:CCNA_00453
         (363 letters)



>NCBI__GCF_000245775.1:WP_008538534.1
          Length = 609

 Score =  120 bits (302), Expect = 7e-32
 Identities = 99/315 (31%), Positives = 154/315 (48%), Gaps = 30/315 (9%)

Query: 66  VVTCARGSSDHAATFARYLIETKAGVLTSSAGPSVSSVYDASPNLEGALYLAISQSGKSP 125
           +V C  G++ HA    +Y IE  A +       S     D   + E  L + ISQSG++ 
Sbjct: 298 IVAC--GTAYHAGLVGKYYIEKLARIPVEIDIASEFRYRDPIID-EHTLTIVISQSGETS 354

Query: 126 DLLAAVKAAKAAGAHAVALVNVVDSPLAALADEVIPLHAGPELSVAATKSYIAALVA--- 182
           D LAA+K +K  GA  +A+ NVV S +A  AD+V+   AGPE++VA+TK+Y   LV    
Sbjct: 355 DTLAALKESKRLGAKTLAITNVVGSSIAREADQVMYTWAGPEIAVASTKAYTTQLVTMFL 414

Query: 183 ----VTQLIAAWTEDA--ELTAALQDLPTALAAAWTLDWSLAVERLKT-------ASNLY 229
               V+ L    T +   EL   L+ LP  +    TL+    VE +KT        ++++
Sbjct: 415 FAMYVSGLKGTITTERTHELLTQLRLLPDEINR--TLE---DVEPIKTFAKNYAFNNDVF 469

Query: 230 VLGRGVGFGVALEAALKFKETCGLHAEAFSAAEVLHGPMALVKDGFPALVFAQNDESRAS 289
            +GR + + VALE +LK KE   +HAEA++A E+ HG +AL++ G P +  A        
Sbjct: 470 YIGRSLDYNVALEGSLKLKEISYIHAEAYAAGELKHGTLALIESGVPVIALATQKSVYEK 529

Query: 290 VDEMAAGLRARGASVLIAGGGGD------APDALPTLASHPVLEPILMIQSFYRMANALS 343
                  ++AR A ++      D          +   A+  +L P+L +     +A   +
Sbjct: 530 TLSNIKEVKARDAVMIGIAAEDDNELEKYVDHVIKVPATDELLIPLLTVVPLQLLAYYAA 589

Query: 344 VARGYDPDSPPHLNK 358
           + RG D D P +L K
Sbjct: 590 ITRGCDVDKPRNLAK 604


Lambda     K      H
   0.315    0.128    0.360 

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: 347
Number of extensions: 16
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: 363
Length of database: 609
Length adjustment: 33
Effective length of query: 330
Effective length of database: 576
Effective search space:   190080
Effective search space used:   190080
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 (21.6 bits)
S2: 51 (24.3 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