GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serA in Sphingomonas koreensis DSMZ 15582

Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate Ga0059261_2669 Ga0059261_2669 Lactate dehydrogenase and related dehydrogenases

Query= curated2:Q58424
         (524 letters)



>FitnessBrowser__Korea:Ga0059261_2669
          Length = 318

 Score =  178 bits (451), Expect = 3e-49
 Identities = 107/289 (37%), Positives = 158/289 (54%), Gaps = 7/289 (2%)

Query: 20  EVGEVEVATGLTKEELLEKIKDADVLVVRSGTKVTRDVI-EKAEKLKVIGRAGVGVDNID 78
           +V   E    +    L + +++ D L      ++TRDVI  +  + ++IG  G G ++ID
Sbjct: 25  DVTRNETDMSMDAAALAQAMREHDALCPTVTDRITRDVILTEGRRARIIGNYGAGFEHID 84

Query: 79  VEAATEKGIIVVNAPDASSISVAELTMGLMLAAARNIPQATASLKRGEWDRKR---FKGI 135
           ++AA E GI V N PD  + + A++ M L+L A R   +    L+ GEW   R     G 
Sbjct: 85  LDAAREAGIAVTNTPDVLTDATADIAMTLILMATRRAGEGERELRAGEWTGWRPTHLLGR 144

Query: 136 ELYGKTLGVIGLGRIGQQVVKRAKAFGMNIIGYDPYIPKEVAESMGVELVDDINELCKRA 195
            L GK LG++G GRI + V  RAKAFGM I  +     ++V E+   +    +  L   A
Sbjct: 145 SLRGKVLGLVGYGRIARAVADRAKAFGMKIAVHSRSRAEDVPET---DYHASLQSLLSIA 201

Query: 196 DFITLHVPLTPKTRHIIGREQIALMKKNAIIVNCARGGLIDEKALYEALKEGKIRAAALD 255
           D ++LH P    TRH+I    ++ MK++A++VN  RG LIDE AL EALK G I AA LD
Sbjct: 202 DVVSLHAPGGAATRHMIDAAALSAMKRDAVLVNTGRGTLIDEAALAEALKVGTIAAAGLD 261

Query: 256 VFEEEPPKDNPLLTLDNVIGTPHQGASTEEAQKAAGTIVAEQIKKVLRG 304
           V+E EP  +  L+ L N +  PH G++T E ++A G  VA+ +     G
Sbjct: 262 VYEREPAVEAALIDLPNAVLLPHFGSATLETREAMGMKVADNLDAFFAG 310


Lambda     K      H
   0.316    0.137    0.372 

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: 361
Number of extensions: 16
Number of successful extensions: 4
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: 524
Length of database: 318
Length adjustment: 31
Effective length of query: 493
Effective length of database: 287
Effective search space:   141491
Effective search space used:   141491
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 (21.5 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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