GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdh in Rhodococcus qingshengii djl-6-2

Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate WP_003942060.1 C1M55_RS09025 iron-containing alcohol dehydrogenase

Query= ecocyc::EG12293-MONOMER
         (383 letters)



>NCBI__GCF_002893965.1:WP_003942060.1
          Length = 401

 Score =  320 bits (819), Expect = 6e-92
 Identities = 167/378 (44%), Positives = 242/378 (64%), Gaps = 1/378 (0%)

Query: 6   FFIPSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVIY 65
           F  P + V G  SL +A +    +G  R  +VTD  L   G   +++  L E+ + + ++
Sbjct: 25  FHAPEI-VFGIGSLVEAAHATLRFGGFRPFLVTDPGLIDAGWVSELEDHLTEQGLTATVW 83

Query: 66  DGTQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGDIRDYEGVDR 125
            G  PNP    +AAG ++ +E  CD +I+LGGGS  D AKG+A++AANGG+I DYEGVD+
Sbjct: 84  SGLTPNPKDFEIAAGFEVYQEGECDVIIALGGGSVIDAAKGVAVLAANGGNILDYEGVDQ 143

Query: 126 SAKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLMIGMPK 185
           + KP  P++ + TT+GT +++++FCI+TD  R  K+ I+ + + P ++V D  L+  MP+
Sbjct: 144 ATKPIPPLVMVPTTSGTGADVSQFCIVTDTTRGTKITIIGRALVPDVTVIDPRLLTTMPE 203

Query: 186 SLTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKAREAMAY 245
            L AATG+DALTH IEA+VS+A  P+TD  AL+AV ++ ENL   ++D    +AR  MA 
Sbjct: 204 WLNAATGLDALTHGIEAFVSLAHNPLTDHHALRAVGLVTENLVHTIQDPMEMEARSVMAQ 263

Query: 246 AQFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAARLRDCAA 305
           A   AG+AF NA LG  HAM+HQ+GG  +LPHGV N +LLPHV  FNS   AA     AA
Sbjct: 264 ASLEAGLAFTNAILGAAHAMSHQVGGMLDLPHGVINGILLPHVIRFNSTTDAAPFVAIAA 323

Query: 306 AMGVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDLNVKEEDFAVLATNALKDACGFT 365
           A+ +        E A A  + +  LA++V +P GL +L V+EED + LA+ AL DAC  T
Sbjct: 324 ALSLPEQRGTPEEAALAVADRVERLAREVGVPKGLGELGVREEDLSRLASFALLDACMST 383

Query: 366 NPIQATHEEIVAIYRAAM 383
           NP +AT E++VA++R A+
Sbjct: 384 NPREATQEQMVALFRGAL 401


Lambda     K      H
   0.318    0.131    0.373 

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: 401
Number of extensions: 20
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: 383
Length of database: 401
Length adjustment: 31
Effective length of query: 352
Effective length of database: 370
Effective search space:   130240
Effective search space used:   130240
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 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