GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdh in Methanobacterium veterum MK4

Align L-threonine 3-dehydrogenase; TDH; EC 1.1.1.103 (uncharacterized)
to candidate WP_048080142.1 EJ01_RS01405 hypothetical protein

Query= curated2:Q82MN2
         (342 letters)



>NCBI__GCF_000745485.1:WP_048080142.1
          Length = 399

 Score =  100 bits (249), Expect = 6e-26
 Identities = 93/317 (29%), Positives = 146/317 (46%), Gaps = 54/317 (17%)

Query: 1   MKALVKEKAEPGLWLMDVPEPEIG-PGDVLIKVLRTGICGTDLHIRSWDGWAQQAVRTPL 59
           MKA+V  K    + + DV  P+I  P D ++++  + ICG+DLH+  +DG  +    +  
Sbjct: 1   MKAVVY-KGPKNVEVEDVENPKISKPTDAIVRITSSAICGSDLHM--YDG--ETTFESGR 55

Query: 60  VLGHEFVGEVVETGRDVVDIKAGDRVSGEGHLVCGKCRNCQAGRRHLCRAT--------- 110
            LGHE +G V E G  V  +K GDRV    ++ CG C NC  G  + C            
Sbjct: 56  TLGHEPMGVVEEVGDAVQLVKPGDRVVMPFNIACGFCLNCIQGLTNACLTLNPDQPGSAY 115

Query: 111 --VGLGVGRDGAFAEYVALPAANVWVHRVP------VDLDVAAIFDPFGNAVH-TALSFP 161
             V +G  + G  AEYV +P A+    ++P       + D   + D F  + + T L+  
Sbjct: 116 GYVNMGPYQGGQ-AEYVLVPYADWACLKLPGEPGDEFEDDFVLLADIFPTSYYSTELANV 174

Query: 162 LVGEDVLITGAGPIGLMAAAVARHAGARNVMITDVSEERLELARKIGVSLALNVADTTIA 221
            +G+ V + GAGP+GL+AA  A   GA  V I D SEERL+ A  IG ++ +N  D   A
Sbjct: 175 SIGKAVAVFGAGPVGLLAAYSAILKGASEVYIIDDSEERLKRAESIG-AIPINTDDGDPA 233

Query: 222 D-------------------GQRALGLREGFD-IGLE--------MSGRPEAMRDMIANM 253
                                ++ LG+    D +G +           R + + D+   +
Sbjct: 234 QQIMEIRQNNKNLMESLRPGEEKTLGVDSAIDAVGFQAYDRDNPNQEKRNQVLMDIANVI 293

Query: 254 THGGRIAMLGLPSQEFP 270
             GG + ++G+  +E P
Sbjct: 294 NAGGHVGLIGVYPKENP 310


Lambda     K      H
   0.322    0.140    0.431 

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: 316
Number of extensions: 13
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: 342
Length of database: 399
Length adjustment: 30
Effective length of query: 312
Effective length of database: 369
Effective search space:   115128
Effective search space used:   115128
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 (21.9 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