GapMind for Amino acid biosynthesis

 

Aligments for a candidate for hisN in Shewanella sp. ANA-3

Align alkaline phosphatase (EC 3.1.3.1) (characterized)
to candidate 7026304 Shewana3_3446 alkaline phosphatase (RefSeq)

Query= BRENDA::P00634
         (471 letters)



>lcl|FitnessBrowser__ANA3:7026304 Shewana3_3446 alkaline phosphatase
           (RefSeq)
          Length = 464

 Score =  156 bits (394), Expect = 2e-42
 Identities = 114/328 (34%), Positives = 160/328 (48%), Gaps = 58/328 (17%)

Query: 65  KNIILLIGDGMGDSEITAARNYAEGAGGFFKGIDALPLTGQYTHYALNKKTGKPDYVTDS 124
           KNI+++IGDGMG S  +A R Y +      + ++           A         YVTDS
Sbjct: 41  KNIVIMIGDGMGPSYTSAYRYYKDNPDT--EEVEQTVFDRLLVGMASTYPASVSGYVTDS 98

Query: 125 AASATAWSTGVKTYNGALGVDIHEKDHPTILEMAKAAGLATGNVSTAELQDATPAALVAH 184
           AA+ATA +TGVK+YNGA+ VD  ++  PTI E AK  GL+TG   T+++  ATPAA ++H
Sbjct: 99  AAAATALATGVKSYNGAISVDTQKQPLPTIFEKAKTLGLSTGVAVTSQINHATPAAFLSH 158

Query: 185 VTSRKCYGPSATSEKCPGNALEKGGKGSITEQLLNARADVTLGGGAKTFAETATAGEWQG 244
             SRK Y   A S                    L   ADV LGGG K F     A     
Sbjct: 159 NESRKNYDALALS-------------------YLETNADVFLGGGQKYFPPELLA----- 194

Query: 245 KTLREQAQARGYQLVSDAASLNSVTEANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKP 304
                Q  A+GYQ ++    L S+T    Q  +LGLFA+  +P  W          ID+ 
Sbjct: 195 -----QFTAKGYQHITRFDDLASIT----QPKVLGLFAEVQLP--WA---------IDE- 233

Query: 305 AVTCTPNPQRNDSVPTLAQMTDKAIELLSKNEKGFFLQVEGASIDKQDHAANPCGQIGET 364
                           L+ +T KA+ LLS+NE+GF L VEG+ ID   H  +    +GE 
Sbjct: 234 -----------KDAKKLSTLTQKALSLLSQNEQGFVLLVEGSLIDWAGHNNDIAAAMGEM 282

Query: 365 VDLDEAVQRALEFAKKEGNTLVIVTADH 392
            +   A++   +F ++  +TL+++TADH
Sbjct: 283 DEFANAIEVVEQFVRQNPDTLMVITADH 310


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: 515
Number of extensions: 25
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 471
Length of database: 464
Length adjustment: 33
Effective length of query: 438
Effective length of database: 431
Effective search space:   188778
Effective search space used:   188778
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: 51 (24.3 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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