GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serB in Lentibacillus jeotgali Grbi

Align Phosphoserine phosphatase; PSP; EC 3.1.3.3 (characterized)
to candidate WP_010529737.1 ON01_RS04145 HAD family hydrolase

Query= SwissProt::P94512
         (260 letters)



>NCBI__GCF_000224785.1:WP_010529737.1
          Length = 261

 Score =  278 bits (710), Expect = 1e-79
 Identities = 136/260 (52%), Positives = 178/260 (68%), Gaps = 2/260 (0%)

Query: 1   MKAVFFDLDDTLLWDEKSVRTTFAETCLQAEKKYGLAPEEFEAAVREAARELYMSYETYP 60
           +K + FDLDDTL+WDEKS+   F   C  A +K    P   E  +RE A+ L+ SY+TY 
Sbjct: 2   LKTIMFDLDDTLIWDEKSIDEAFKAACRLAAQKSDADPNLLETKIREHAQSLFASYDTYE 61

Query: 61  YTVMIGINPFEGLWSNFSEPISEGFQKLNKIVPEYRRNAWTNGLKALGIDDPAYGEYLGE 120
           +T MIGI+PFEGLW  F +   E F++LN+I P YR+ +W   LK  G+DDP  G  L E
Sbjct: 62  FTEMIGISPFEGLWGEFDDE-GESFRQLNEIAPIYRKESWAKALKEAGVDDPQLGLELAE 120

Query: 121 FFAAERRKRPFVYDETFAVLDQLKGKYELLLLTNGDPSLQKEKLAGVPELAPYFNEIVIS 180
            F  ERRK  +V++ETF VL++L+G Y+LL+LTNG P LQ+ KL   PE+ PYF+ IVIS
Sbjct: 121 AFQEERRKNQYVFEETFDVLNKLRGDYQLLMLTNGSPDLQQTKLNITPEIKPYFDHIVIS 180

Query: 181 GAFGKGKPDVSIFEHCLKLMNIEKDDAIMVGDNLNTDILGASRAGIKTVWINRTDKKNET 240
           GAFGKGKPD SIF+H L L++ EKD+ +MVGDN N+DILGASRAG+++VWIN   K    
Sbjct: 181 GAFGKGKPDPSIFDHALSLLSAEKDEVLMVGDNPNSDILGASRAGVQSVWINH-QKYEIG 239

Query: 241 DVKPDYIISSLHDLFPILEK 260
           D  P + I+ L +L  +L K
Sbjct: 240 DNNPTFEITRLEELLEVLAK 259


Lambda     K      H
   0.318    0.138    0.409 

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: 262
Number of extensions: 8
Number of successful extensions: 2
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: 260
Length of database: 261
Length adjustment: 25
Effective length of query: 235
Effective length of database: 236
Effective search space:    55460
Effective search space used:    55460
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 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

Links

Downloads

Related tools

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