GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serA in Klebsiella michiganensis M5al

Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate BWI76_RS26540 BWI76_RS26540 D-isomer specific 2-hydroxyacid dehydrogenase family protein

Query= curated2:O27051
         (525 letters)



>FitnessBrowser__Koxy:BWI76_RS26540
          Length = 317

 Score =  210 bits (534), Expect = 7e-59
 Identities = 121/309 (39%), Positives = 191/309 (61%), Gaps = 7/309 (2%)

Query: 5   KVLIADSINEKGISELEEVAEVVVNTT-ITPEELLDAIKDFDAIVVRSRTKVTREVIEAA 63
           K+L+   I  +G   LE     ++N + +  E+++  I D D I+VR  +K++  V EAA
Sbjct: 4   KILLPQEIMAEGREYLESRGYQLINGSGMEEEDIIRDIGDCDGIIVRL-SKMSDRVFEAA 62

Query: 64  PRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKIAIA-DR 122
            +LK++AR G G D VD+++A   G++V+NAP + S++VAE +I  ML  +R   +  ++
Sbjct: 63  KKLKVVARHGAGYDTVDLESAKRHGVVVLNAPIANSMSVAELAIFYMLHCSRNFKLVQEK 122

Query: 123 SVKEGKWEKNRFMGIELNGKTLGIIGMGRIGSQVVVRT-KAFGMDIMVYDPYISKEAAEE 181
            +++  W K R   +EL+GKTLG+IG+G IGS+V ++    F M ++ YDPY +++   E
Sbjct: 123 MLEDYYWAKLRTPKVELDGKTLGLIGVGNIGSRVAIKALHGFNMKVIAYDPYKTQQQIPE 182

Query: 182 MGVTVT-DLETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARGGIIDEDA 240
            GV +T D + +  ESD V++H P T ET   + E +F +MK +A+ +N ARG ++DE A
Sbjct: 183 -GVELTDDFDRIFTESDFVSLHCPTTAETTDFVGEKQFSMMKPSAYFINTARGKLVDEKA 241

Query: 241 LYRALKDGEIAGAALDVFEEEPPEGS-PLLELENVVLTPHIGASTSEAQRDAAIIVANEI 299
           LY AL    IAGA +DV ++EP + + P+  L N+V+ PHIGA+T EA   A++  A  I
Sbjct: 242 LYHALSTHAIAGAGVDVLKKEPFDANDPIFSLSNIVIAPHIGAATIEATDRASLHSAIGI 301

Query: 300 KTVFQGGAP 308
             V  G  P
Sbjct: 302 DEVLSGKKP 310


Lambda     K      H
   0.316    0.135    0.366 

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: 395
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: 525
Length of database: 317
Length adjustment: 31
Effective length of query: 494
Effective length of database: 286
Effective search space:   141284
Effective search space used:   141284
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