GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdh in Pseudomonas fluorescens FW300-N2E3

Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate AO353_17425 AO353_17425 lactaldehyde reductase

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



>FitnessBrowser__pseudo3_N2E3:AO353_17425
          Length = 382

 Score =  513 bits (1321), Expect = e-150
 Identities = 260/379 (68%), Positives = 304/379 (80%)

Query: 4   STFFIPSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSV 63
           STFFIP+VN++G   L +AMN + +YGF + LIVTD  L K G+AG + + L  ++I SV
Sbjct: 3   STFFIPAVNIMGTGCLDEAMNAIRNYGFRKALIVTDAGLAKAGVAGLIAEKLAMQDIDSV 62

Query: 64  IYDGTQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGDIRDYEGV 123
           I+DG +PNP+  NV +GL+LL+ + CD VISLGGGSPHDCAKGIAL A NGG I DYEGV
Sbjct: 63  IFDGAKPNPSIANVESGLELLQRSQCDCVISLGGGSPHDCAKGIALCATNGGKIADYEGV 122

Query: 124 DRSAKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLMIGM 183
           D+SAKPQLP+IAINTTAGTASEMTRFCIITDE+RH+KMAIVD++VTPLLSVND +LM  M
Sbjct: 123 DQSAKPQLPLIAINTTAGTASEMTRFCIITDESRHVKMAIVDRNVTPLLSVNDPALMAAM 182

Query: 184 PKSLTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKAREAM 243
           PK LTAATGMDALTHAIEAYVS AA PITDACALKA+ +I+ NL LAV DGS+  ARE M
Sbjct: 183 PKGLTAATGMDALTHAIEAYVSTAANPITDACALKAIELISRNLRLAVHDGSDMIARENM 242

Query: 244 AYAQFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAARLRDC 303
           AYAQFLAGMAFNNASLG+VHAMAHQLGGFY+LPHGVCNAVLLPHVQ FN+ V A RL   
Sbjct: 243 AYAQFLAGMAFNNASLGFVHAMAHQLGGFYDLPHGVCNAVLLPHVQSFNAAVCAERLAVV 302

Query: 304 AAAMGVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDLNVKEEDFAVLATNALKDACG 363
           A A+G +  G +  EGA+A I AIR LA+ V+IP GLRDL  K +D  +LA NALKDACG
Sbjct: 303 AQALGADTLGVSPEEGAQAAIVAIRALARDVEIPGGLRDLGAKLQDIPILAANALKDACG 362

Query: 364 FTNPIQATHEEIVAIYRAA 382
            TNP  A   +I  I+R+A
Sbjct: 363 LTNPRAADQRQIEEIFRSA 381


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: 531
Number of extensions: 17
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: 382
Length adjustment: 30
Effective length of query: 353
Effective length of database: 352
Effective search space:   124256
Effective search space used:   124256
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