GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdh in Pseudomonas stutzeri RCH2

Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate GFF3713 Psest_3782 Alcohol dehydrogenase, class IV

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



>FitnessBrowser__psRCH2:GFF3713
          Length = 388

 Score =  252 bits (643), Expect = 1e-71
 Identities = 142/377 (37%), Positives = 213/377 (56%), Gaps = 5/377 (1%)

Query: 8   IPSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVIYDG 67
           +P +  +GA +      ++ + G  R LIVTD M+ +LG    +   L E  I S  +  
Sbjct: 7   LPRLMEVGAGASQQLARVLKELGCNRPLIVTDRMMVELGYVARIAGQLGEAGIASQCFAD 66

Query: 68  TQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGDIRDYEGVDRSA 127
           T P PT  ++ AG++++++ + DS+++LGGGSP D AK I ++   GG++RDY      +
Sbjct: 67  TLPEPTAASIRAGVEMVRQGDFDSIVALGGGSPIDSAKAIGILGKFGGEMRDYRFPRDVS 126

Query: 128 KPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLMIGMPKSL 187
           +  LP+IAI TTAGT SE TRF IITDE    KM        P+ ++ D  L + +P  +
Sbjct: 127 EAGLPLIAIPTTAGTGSEATRFTIITDETSDEKMLCAGLGFMPIAALIDYELTLSLPPRV 186

Query: 188 TAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKAREAMAYAQ 247
           TA TG+DALTHAIEAYVS  A+  +DA AL+A+ ++A NL  A  +  N  AREAM    
Sbjct: 187 TADTGIDALTHAIEAYVSRKASLYSDAQALEAMRLLAPNLRAAFHEPGNRAAREAMMLGA 246

Query: 248 FLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAARLRDCAAAM 307
            LAG+AF+NAS+  VH M+  +G F+++PHG+ NA+LLP +  F+   A  R  DCA AM
Sbjct: 247 TLAGIAFSNASVALVHGMSRPIGAFFHVPHGLSNAMLLPAITAFSIPAAPERYADCARAM 306

Query: 308 GVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDLNVKEEDF----AVLATNALKDACG 363
           GV     +     +  +  +R + +++ +P+      +  E F      +A  AL     
Sbjct: 307 GVAAQTDSVGVANDKLLAELRAINQELQVPSP-EQFGISRERFFELRETMARQALASGSP 365

Query: 364 FTNPIQATHEEIVAIYR 380
             NP   T  EI+ +Y+
Sbjct: 366 GNNPRVPTEAEIIDLYK 382


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: 372
Number of extensions: 15
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: 388
Length adjustment: 30
Effective length of query: 353
Effective length of database: 358
Effective search space:   126374
Effective search space used:   126374
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 17 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