GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapE in Klebsiella michiganensis M5al

Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 (characterized)
to candidate BWI76_RS14620 BWI76_RS14620 acetylornithine deacetylase or succinyl-diaminopimelate desuccinylase

Query= SwissProt::Q9JYL2
         (381 letters)



>FitnessBrowser__Koxy:BWI76_RS14620
          Length = 370

 Score =  114 bits (285), Expect = 4e-30
 Identities = 86/279 (30%), Positives = 131/279 (46%), Gaps = 16/279 (5%)

Query: 4   TQSLELAKELISRPSVTP--DDRDCQKLLAERLHKIGFAAEELHFGDTKN---IWLRRGT 58
           T +LELA++L+   ++ P   + DC +  A+ L+  GFA     FG++++    WL   T
Sbjct: 2   TTTLELARQLLGFNTINPPGSEADCMRYFADWLNANGFAVSLSSFGESRSNLIAWLPGAT 61

Query: 59  KAPVVCFAGHTDVVPTGPVEKWDSPPFEPAERDGRLYGRGAADMKTSIACFVTACERFVA 118
               + F GH D VP G   +W   PF     DGRLYGRG++DMK +IA F  AC +   
Sbjct: 62  PGKPLAFTGHLDTVPLGNA-RWRYDPFGSQMEDGRLYGRGSSDMKAAIAAFAVACVQQRE 120

Query: 119 KHPNHQGSIALLITSDEEGDALDGTTKVVDVLKARDELIDYCIVGEPTAVDKLGDMIKNG 178
                +G++ LLIT  EE    DG   +  +  A    +   IVGEPTA     +    G
Sbjct: 121 TILAGRGAV-LLITGGEE-TGCDGARAL--IASAPLPEVGALIVGEPTA-----NYPVIG 171

Query: 179 RRGSLSGNLTVKGKQGHIAYPHLAINPVHTFAPALLELTQEVWDEGNEYFPPTSFQISNI 238
            +G+L      +GK  H A P L IN ++  A AL ++        +      +  +  I
Sbjct: 172 HKGALWLRCETRGKTAHGAMPELGINAIYLAADALAKIQHFSPGAPHPLMKQPTVNVGRI 231

Query: 239 NGGTGATNVIPGELNVKFNFRFSTESTEAGLKQRVHAIL 277
            GG    N +P       + R + +   A ++QR+  +L
Sbjct: 232 EGGLN-INSVPDRTRFDVDIRSAPDLQHATIRQRLTTLL 269


Lambda     K      H
   0.317    0.135    0.400 

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: 345
Number of extensions: 20
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: 381
Length of database: 370
Length adjustment: 30
Effective length of query: 351
Effective length of database: 340
Effective search space:   119340
Effective search space used:   119340
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