GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Pseudomonas fluorescens FW300-N1B4

Align phosphoserine aminotransferase; EC 2.6.1.52 (characterized)
to candidate Pf1N1B4_351 Phosphoserine aminotransferase (EC 2.6.1.52)

Query= CharProtDB::CH_002572
         (362 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_351
          Length = 292

 Score =  322 bits (826), Expect = 6e-93
 Identities = 164/294 (55%), Positives = 202/294 (68%), Gaps = 2/294 (0%)

Query: 69  VLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFDAKVTVDGL 128
           VLF  GG   QFA +PLN+L +  TADY+D G W+  AI+EA +Y   NV       D  
Sbjct: 1   VLFLQGGASQQFAQIPLNLLPESGTADYIDTGIWSQKAIEEASRYGHVNVAATAKPYDYF 60

Query: 129 RAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTILSRPIDVSR 188
            A+    EW+LS +AAY+HY PNETI G+     P+ G DV + AD SS ILSRP+DVSR
Sbjct: 61  -AIPGQNEWKLSKDAAYVHYAPNETIGGLEFQWIPETG-DVPLVADMSSDILSRPVDVSR 118

Query: 189 YGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNTPPTFAWYL 248
           +G+IYAGAQKNIGP+G+ + IVREDLLG A   CP++L+Y +  DNGSM+NTPPT AWYL
Sbjct: 119 FGMIYAGAQKNIGPSGIVVNIVREDLLGHARSICPTMLNYKVAADNGSMYNTPPTLAWYL 178

Query: 249 SGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSRMNVPFQLADSA 308
           SGLVF+WLK  GGV  + K+N+ K   LY  ID S  Y N + K++RS MNVPF+LAD  
Sbjct: 179 SGLVFEWLKEQGGVEAIGKLNEVKQRTLYDFIDASGLYSNPINKSDRSWMNVPFRLADDR 238

Query: 309 LDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFERRHG 362
           LDK FL  +   GL  LKGHR VGGMRASIYNA+ +  V AL  +M EFE+ HG
Sbjct: 239 LDKPFLAGADERGLLNLKGHRSVGGMRASIYNAVDIVAVNALVSYMAEFEKEHG 292


Lambda     K      H
   0.319    0.136    0.405 

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: 339
Number of extensions: 11
Number of successful extensions: 3
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: 362
Length of database: 292
Length adjustment: 28
Effective length of query: 334
Effective length of database: 264
Effective search space:    88176
Effective search space used:    88176
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 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