GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serB in Phyllobacterium brassicacearum STM 196

Align Phosphoglycerate mutase (characterized, see rationale)
to candidate WP_106712249.1 CU102_RS16835 histidine phosphatase family protein

Query= uniprot:P72649
         (349 letters)



>NCBI__GCF_003010955.1:WP_106712249.1
          Length = 192

 Score = 65.1 bits (157), Expect = 1e-15
 Identities = 58/195 (29%), Positives = 89/195 (45%), Gaps = 15/195 (7%)

Query: 133 LLLIRHGETQWNREGRFQGIRDIPLNDNGRHQAQKAAEFLKDVPINLGISSPMARPKETA 192
           + L+RHGET+W+  G+  G  DIPL   G   A+K A  L  +  +   SSP  R   TA
Sbjct: 7   IYLVRHGETEWSASGKHTGRTDIPLTAAGEEAARKLAGRLDGIAYSAVWSSPSQRAANTA 66

Query: 193 EIILQYHPSIELDLQPELAEICHGLWEGKLETEIEAEYPGLLQQWKDAPATVQMPEGENL 252
            ++  + P+ E   + ELAE  +G +EG    +I AE P + Q ++D       P GE  
Sbjct: 67  -VLAGFGPATE--KKAELAEWDYGAYEGITTKQILAERP-VWQLFRDG-----CPNGEAA 117

Query: 253 QQVWDRAIACWQDRVKFYSQGDGSTVGIVVAHDAINKVILAYLLGLTPAHFWQVKQGNGG 312
             V  RA     D +    +   +TV ++ +     +V+ A  LG    H          
Sbjct: 118 LDVGLRA-----DIIIGQLRSANNTV-LIFSSSHFLRVLAARWLGSPAEHGAHFVLDTAS 171

Query: 313 VSVIDYPQGLDKPPV 327
           +SV+ Y   L +P +
Sbjct: 172 ISVLGYEHDLTEPVI 186



 Score = 26.6 bits (57), Expect = 6e-04
 Identities = 15/53 (28%), Positives = 24/53 (45%)

Query: 54  AAGQTLLIVAHNGINRCLLMSAIGMPASHYQRLQQSNCNINVLNFSGGWGDPV 106
           +A  T+LI + +   R L    +G PA H         +I+VL +     +PV
Sbjct: 133 SANNTVLIFSSSHFLRVLAARWLGSPAEHGAHFVLDTASISVLGYEHDLTEPV 185


Lambda     K      H
   0.319    0.136    0.424 

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: 209
Number of extensions: 13
Number of successful extensions: 3
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: 349
Length of database: 192
Length adjustment: 24
Effective length of query: 325
Effective length of database: 168
Effective search space:    54600
Effective search space used:    54600
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 (21.7 bits)
S2: 47 (22.7 bits)

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

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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