GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serA in Sphingomonas koreensis DSMZ 15582

Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate Ga0059261_1479 Ga0059261_1479 Lactate dehydrogenase and related dehydrogenases

Query= BRENDA::Q9Z564
         (529 letters)



>FitnessBrowser__Korea:Ga0059261_1479
          Length = 332

 Score =  186 bits (473), Expect = 9e-52
 Identities = 113/320 (35%), Positives = 176/320 (55%), Gaps = 9/320 (2%)

Query: 3   SKPVVLIAEELSPATVDALGPDFEI---RHCNGADRAELLPAIADVDAILVRSATKVDAE 59
           ++P V +  EL  A    +G  F+    +     DRA LL A+AD D ++      +DA+
Sbjct: 8   ARPRVAVTRELPDAIAARMGELFDTSFNQSDEAMDRAALLAAVADCDVLVPTVTDTIDAD 67

Query: 60  AVAAA-KKLKVVARAGVGLDNVDVSAATKAGVMVVNAPTSNIVTAAELACGLIVATARNI 118
            +AAA ++LK++A  G G++++D+ AA   G++V N P       A++   LIV+  R +
Sbjct: 68  LIAAAGERLKLIANFGSGVNHIDLKAARARGIVVTNTPGVLTEDTADMTMALIVSVPRRL 127

Query: 119 PQANAALKNGEWKRSKYTGV---ELAEKTLGVVGLGRIGALVAQRMSAFGMKVVAYDPYV 175
            +    +++G+WK     G+    +  K LG+VG+GRIG  VA+R  AFG+ +  ++ + 
Sbjct: 128 AEGEKLVRSGQWKGWSPGGMLGHRIGGKKLGIVGMGRIGQAVARRARAFGLSIHYHNRHR 187

Query: 176 QPARA-AQMGVKVLS-LDELLEVSDFITVHLPKTPETLGLIGDEALRKVKPSVRIVNAAR 233
            P    A++G      LD +L   D +T+H P   E+  LI    +  + P V ++NA+R
Sbjct: 188 LPEVVEAELGAAWHGDLDAMLREIDILTIHTPLNEESRDLIDARRIGLLGPQVYLINASR 247

Query: 234 GGIVDEEALYSALKEGRVAGAGLDVYAKEPCTDSPLFEFDQVVATPHLGASTDEAQEKAG 293
           GGIVDEEA+  AL+ GR+AGAGLDV+  EP  D  L     VV TPH+G++T E +   G
Sbjct: 248 GGIVDEEAMVDALEAGRLAGAGLDVWRFEPQIDPRLLALPNVVMTPHMGSATYEGRHATG 307

Query: 294 IAVAKSVRLALAGELVPDAV 313
             V  ++R    G   PD V
Sbjct: 308 EKVIANIRFWADGHRPPDQV 327


Lambda     K      H
   0.315    0.133    0.362 

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: 399
Number of extensions: 22
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: 529
Length of database: 332
Length adjustment: 32
Effective length of query: 497
Effective length of database: 300
Effective search space:   149100
Effective search space used:   149100
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 (21.6 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