GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Sphingobium czechense LL01

Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase; Vegetative protein 43; VEG43 (uncharacterized)
to candidate WP_066602966.1 V473_RS09375 NADP-dependent malic enzyme

Query= curated2:P39646
         (323 letters)



>NCBI__GCF_001046645.1:WP_066602966.1
          Length = 755

 Score =  143 bits (361), Expect = 1e-38
 Identities = 95/324 (29%), Positives = 151/324 (46%), Gaps = 6/324 (1%)

Query: 4   LFSTVQEKVAGKDVKIVFPEGLDERILEAVSKLAGNKVLNPIVIGNENEIQAKAKELNLT 63
           L   V E   G   +I + EG D+R+L A+       ++ P V+     +  K  EL L+
Sbjct: 427 LMLPVFEAARGTGCRIAYGEGEDDRVLRAIRDALDEGIVRPTVVARRRILAQKLPELGLS 486

Query: 64  LG---GVKIYDPHT-YEGMEDLVQAF--VERRKGKATEEQARKALLDENYFGTMLVYKGL 117
                 V++ DP T +  M +LV+A+  V  R+G   +E  R           ML+  G 
Sbjct: 487 FDLDRDVEVIDPETDHLVMGELVEAYRTVASRRGVPADEILRHVYRRPTITAAMLLQTGR 546

Query: 118 ADGLVSGAAHSTADTVRPALQIIKTKEGVKKTSGVFIMARGEEQYVFADCAINIAPDSQD 177
            D  + G        V   L+II    G  +   +  +          D  +   P  + 
Sbjct: 547 VDAALVGGRSEYWGQVEHVLRIIDRTPGHSRVYALSGLILDAGALFITDTHMVPDPTPEQ 606

Query: 178 LAEIAIESANTAKMFDIEPRVAMLSFSTKGSAKSDETEKVADAVKIAKEKAPELTLDGEF 237
           +AE+ + +A   + F + PR A+LS S  G++ +D   K+  A KI ++ APEL +DGE 
Sbjct: 607 IAEMTLLAATEIQHFGLTPRAALLSHSNFGASHTDSARKMRKAFKIVRDAAPELAVDGEM 666

Query: 238 QFDAAFVPSVAEKKAPDSEIKGDANVFVFPSLEAGNIGYKIAQRLGNFEAVGPILQGLNM 297
             DAA   ++ E+  PDS  +G AN+ V P+L+A NI         +   VGP+L GL+ 
Sbjct: 667 HADAALSQALRERLIPDSRFEGPANLLVMPNLDAANITLTALSASSSSPTVGPMLMGLSK 726

Query: 298 PVNDLSRGCNAEDVYNLALITAAQ 321
           P++ L+ G  +  + NL  I AA+
Sbjct: 727 PIHVLTPGVTSRGILNLTAIAAAE 750


Lambda     K      H
   0.314    0.132    0.359 

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: 456
Number of extensions: 19
Number of successful extensions: 1
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: 323
Length of database: 755
Length adjustment: 34
Effective length of query: 289
Effective length of database: 721
Effective search space:   208369
Effective search space used:   208369
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.

Links

Downloads

Related tools

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