GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galT in Pontibacter ramchanderi LP43

Align UTP--hexose-1-phosphate uridylyltransferase (EC 2.7.7.10) (characterized)
to candidate WP_101446337.1 BD749_RS16425 UDP-glucose--hexose-1-phosphate uridylyltransferase

Query= reanno::Cola:Echvi_0695
         (347 letters)



>NCBI__GCF_002846395.1:WP_101446337.1
          Length = 344

 Score =  457 bits (1175), Expect = e-133
 Identities = 201/338 (59%), Positives = 253/338 (74%)

Query: 1   MTDFNFEDHSHRRYNPFTGDWLQVSPHRGKRPWQGQEEDTAEAQKPAYDEKCYLCPGNTR 60
           M  F+  +H HRR+NP TG+W+ VSPHR KRPWQGQ+E+     +PAYD  CYLCPGNTR
Sbjct: 1   MATFDLAEHPHRRFNPLTGEWVLVSPHRSKRPWQGQQEEQPHDSRPAYDPTCYLCPGNTR 60

Query: 61  INGEKNPDYTGAYVFQNDFGALTSDIPQGEMSEGEFFRAKSERGICKVICFSPRHDLTIP 120
            +GE+NP Y   +VF NDFGAL   IP+G    G+  RA+SERGIC+VICFSPRHDLT+ 
Sbjct: 61  ASGEQNPAYATTFVFNNDFGALQDGIPEGAYVAGDLIRAESERGICRVICFSPRHDLTLA 120

Query: 121 ELDVQAITKVVELWKKEYQELGGKDFINHVQIFENKGSVMGCSNPHPHGQIWAQESIPVE 180
           E+    I KVV+LW+KEY EL   D+IN+VQIFENKGS+MGCSNPHPHGQ+WAQ ++PVE
Sbjct: 121 EMSTADIRKVVDLWQKEYAELSSLDYINYVQIFENKGSIMGCSNPHPHGQVWAQSTVPVE 180

Query: 181 PAKKQVKFGEYYQKYGRSMVLDYVYEELKKGERILFENDYFVGLVPFWAVWPFEAMIAPK 240
           PAK+  +  +Y+  + RS++ DY+  ELK  ER++ EN++FV LVPFWAVWPFE ++  K
Sbjct: 181 PAKETTQQAQYFAHHSRSLLADYLQLELKLQERVVVENEHFVVLVPFWAVWPFETIVISK 240

Query: 241 THIASLSEMDAAQMEALADAYRQLAIMYDNVFKVSFPYSAGIHQAPTDGQNHPEWDLHMV 300
            H   + +M  A+ +  +   + L + YD VF VSFPYS GIHQ+PTDGQ HP W  HM 
Sbjct: 241 RHFQHIGQMTDAEKDGFSKVLQALTVTYDRVFGVSFPYSCGIHQSPTDGQEHPGWHFHMH 300

Query: 301 FYPPLLRSATVKKFMVGYEMLANPQRDITAESAVKILK 338
           FYPPLLRSATVKKFMVGYEM+ NPQRDIT E+A ++L+
Sbjct: 301 FYPPLLRSATVKKFMVGYEMMGNPQRDITPEAAARVLR 338


Lambda     K      H
   0.319    0.136    0.425 

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: 452
Number of extensions: 10
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: 347
Length of database: 344
Length adjustment: 29
Effective length of query: 318
Effective length of database: 315
Effective search space:   100170
Effective search space used:   100170
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: 49 (23.5 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