GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisN in Shewanella loihica PV-4

Align alkaline phosphatase (EC 3.1.3.1) (characterized)
to candidate 5210798 Shew_3226 alkaline phosphatase (RefSeq)

Query= BRENDA::P00634
         (471 letters)



>FitnessBrowser__PV4:5210798
          Length = 543

 Score =  167 bits (424), Expect = 6e-46
 Identities = 120/349 (34%), Positives = 179/349 (51%), Gaps = 65/349 (18%)

Query: 44  ARRLTGDQTAALRDSLSDKPAKNIILLIGDGMGDSEITAARNYAEGAGGFFKGIDALPLT 103
           A  L G QTA  R        KNI++++GDGMG +  +A R Y +      + I+     
Sbjct: 23  ADNLLGPQTAPSRP-------KNIVIMVGDGMGPAYTSAYRYYQDNPNT--QEIEQTVFD 73

Query: 104 GQYTHYALNKKTGKPDYVTDSAASATAWSTGVKTYNGALGVDIHEKDHPTILEMAKAAGL 163
                 A         YVTDSAA+ATA +TGVKTYNGA+ VDI ++  PT+LE+AK  G+
Sbjct: 74  RLLVGNASTYPAPVSGYVTDSAAAATALATGVKTYNGAVSVDIDKRPVPTLLELAKKRGM 133

Query: 164 ATGNVSTAELQDATPAALVAHVTSRKCYGPSATSEKCPGNALEKGGKGSITEQLLNARAD 223
           +TG   T+++  ATPAA ++H  SR+ Y                    ++ +  L+  AD
Sbjct: 134 STGVTVTSQINHATPAAFLSHNESRRNY-------------------EALAQSYLSTDAD 174

Query: 224 VTLGGGAKTFAETATAGEWQGKTLREQAQARGYQLVSDAASLNSVTEANQQKPLLGLFAD 283
           V LGGG K F++           L +Q +A+GY+++ D+A L  VT    Q  ++GLFAD
Sbjct: 175 VMLGGGQKYFSD----------KLIKQFEAKGYRVLKDSALLEGVT----QPKVMGLFAD 220

Query: 284 GNMPVRWLGPKATYHGNIDKPAVTCTPNPQRNDSVPTLAQMTDKAIELLSKNEKGFFLQV 343
             +P  W          ID+P                L+ MT KA+ELLS+N++GF L V
Sbjct: 221 VQLP--WA---------IDEP------------EARRLSTMTAKALELLSQNDQGFVLLV 257

Query: 344 EGASIDKQDHAANPCGQIGETVDLDEAVQRALEFAKKEGNTLVIVTADH 392
           EG+ ID   H  +    + E  +   A++   ++ ++  +TL++VTADH
Sbjct: 258 EGSLIDWAGHNNDIATAMAEMHEFASAIEVVEQYVRQHQDTLLVVTADH 306


Lambda     K      H
   0.312    0.128    0.365 

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: 568
Number of extensions: 32
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 471
Length of database: 543
Length adjustment: 34
Effective length of query: 437
Effective length of database: 509
Effective search space:   222433
Effective search space used:   222433
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 52 (24.6 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