GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Lutibaculum baratangense AMV1

Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase; Vegetative protein 43; VEG43 (uncharacterized)
to candidate WP_023433704.1 N177_RS17335 NADP-dependent malic enzyme

Query= curated2:P39646
         (323 letters)



>NCBI__GCF_000496075.1:WP_023433704.1
          Length = 761

 Score =  171 bits (432), Expect = 7e-47
 Identities = 105/327 (32%), Positives = 170/327 (51%), Gaps = 9/327 (2%)

Query: 1   MADLFSTVQEKVAGKDVKIVFPEGLDERILEAVSKLAGNKVLNPIVIGNENEIQAKAKEL 60
           M ++FST   K A K  +I+F EG DERIL AV  ++  K+  PI++G  + I+ + K  
Sbjct: 434 MKEIFSTA--KAAPK--RIIFAEGEDERILRAVQVVSEEKLAQPILVGRPSVIETRLKRY 489

Query: 61  NLTLG---GVKIYDPHTYEGMEDLVQAFVER--RKGKATEEQARKALLDENYFGTMLVYK 115
            LT+      +I +P       D V+ F++R  RKG   +               + VY+
Sbjct: 490 GLTIRPGIDFEIVNPEDDPRYRDYVETFLDRTCRKGVTPDLARTLVRTSTTVIAAISVYR 549

Query: 116 GLADGLVSGAAHSTADTVRPALQIIKTKEGVKKTSGVFIMARGEEQYVFADCAINIAPDS 175
           G AD ++ G        +R    II  +EG++  S + ++      Y  AD  +   P S
Sbjct: 550 GEADAMICGVEGRFDSHLRWVRNIIGLREGIRDFSALSLLILPRGAYFLADTFVTHDPGS 609

Query: 176 QDLAEIAIESANTAKMFDIEPRVAMLSFSTKGSAKSDETEKVADAVKIAKEKAPELTLDG 235
            DLA++A  +A   + F + P++A+LS S+ GS+ S+  +K+  AV+I +  APEL ++G
Sbjct: 610 ADLADMARSAAEHVRRFGLTPKIALLSHSSFGSSDSESAQKMRSAVQILRRMAPELEVEG 669

Query: 236 EFQFDAAFVPSVAEKKAPDSEIKGDANVFVFPSLEAGNIGYKIAQRLGNFEAVGPILQGL 295
           E   DAA    +  +  P S + G+ANV + P+L+A NI Y++ + L +   VGPIL G 
Sbjct: 670 EMHGDAALDEVLRNRIFPRSRLTGEANVLILPNLDAANIAYELLKSLADALPVGPILIGA 729

Query: 296 NMPVNDLSRGCNAEDVYNLALITAAQA 322
           N P + L+    A  + N+  +  A+A
Sbjct: 730 NKPAHILTPSVTARGIVNMTAVAVAEA 756


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: 489
Number of extensions: 27
Number of successful extensions: 2
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: 761
Length adjustment: 34
Effective length of query: 289
Effective length of database: 727
Effective search space:   210103
Effective search space used:   210103
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