GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Rhodanobacter denitrificans 2APBS1

Align phosphate acetyltransferase (EC 2.3.1.8) (characterized)
to candidate WP_015448846.1 R2APBS1_RS16920 NADP-dependent malic enzyme

Query= BRENDA::O52593
         (332 letters)



>NCBI__GCF_000230695.2:WP_015448846.1
          Length = 763

 Score =  164 bits (414), Expect = 9e-45
 Identities = 104/331 (31%), Positives = 179/331 (54%), Gaps = 13/331 (3%)

Query: 4   LEQIIERAKSDVKTIVLPESTDLRVIKAASMIMKKGIAKVVLIGNEKEIKSLAGDIDLE- 62
           ++ + ERAKS    +V  E  +  V++A  +++ +G+A+ +LIG  + I+       L  
Sbjct: 431 MKPVFERAKSAPCRLVYAEGEEETVLRAVQVVVDEGLARPILIGRPEVIEKRIHRAGLRI 490

Query: 63  --GVMIED-SLNSE-KLEDYANTLYELRKSKGMTIEAARETIKD-PLYYGVMMVKKGEAD 117
             GV IE  ++N + + +DY    + L + +G+T   A+  ++  P     +MV++GEAD
Sbjct: 491 RPGVDIEICNINFDPRFDDYWRHYHRLMERRGVTPSMAKAVVRSRPTAIAALMVERGEAD 550

Query: 118 GMVAGAVNSTANTLRPALQILKTAPGTKLVSSFFVMVVPNCEYGHNGTFVYADCGLVENP 177
            M+ G V      LR    I+    G    S+   +          GTF Y D  + ++P
Sbjct: 551 AMICGLVGQYQGKLRYIRDIIGLDAGVVEPSAMAAVSTDK------GTFFYLDTHVQDDP 604

Query: 178 DADQLSEIAISASKSFEMLVGAKPQVAMLSYSSYGSAKSELTEKVIKATQLAKEKAPHLA 237
             +Q++E  + AS   + L G  P++A+LS  ++GS  +   +K+ KA +L + +AP L 
Sbjct: 605 CPEQIAEATLQASIRLK-LFGIVPKIALLSGGNFGSRDTCGAKKMRKALELIRARAPRLE 663

Query: 238 IDGELQVDAAIVPEVAKSKAKGSSVAGKANVLIFPDLDAGNIAYKLTQRLAKAEAYGPIT 297
           ++GE+Q DAA+VP + +     S + GKANV +FP+LDA NIAY +T+ L+     GPI 
Sbjct: 664 VEGEMQADAALVPALREKLFPHSRLEGKANVFVFPNLDAANIAYNMTRMLSDGVVIGPIL 723

Query: 298 QGLARPVNDLSRGCSAEDIVGVAAITAVQAQ 328
            G+A+P + L    +   +V ++A+  V+AQ
Sbjct: 724 MGVAKPAHILMPQSTVRRVVNMSAVACVEAQ 754


Lambda     K      H
   0.313    0.129    0.346 

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: 517
Number of extensions: 21
Number of successful extensions: 4
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: 332
Length of database: 763
Length adjustment: 34
Effective length of query: 298
Effective length of database: 729
Effective search space:   217242
Effective search space used:   217242
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 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