GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Herbaspirillum seropedicae SmR1

Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate HSERO_RS23520 HSERO_RS23520 histidinol-phosphate aminotransferase

Query= reanno::BFirm:BPHYT_RS14905
         (370 letters)



>FitnessBrowser__HerbieS:HSERO_RS23520
          Length = 360

 Score =  159 bits (403), Expect = 9e-44
 Identities = 127/375 (33%), Positives = 186/375 (49%), Gaps = 29/375 (7%)

Query: 3   ASFGPSYVRAIAPYIAGKPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASE 62
           + F    V  + PY  G+   ++AR        +VKL +NE+P G    A +A+A+  S+
Sbjct: 2   SKFWSPIVSRLTPYTPGEQ-PKIAR--------LVKLNTNESPYGPSPLALQAIAREVSD 52

Query: 63  -LGRYPDANAFELKAALSERY---GVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQY 118
            L  YP+ +A  LK A++ R+   GV    V +GNGS+++L  A HA ++ G+ I++   
Sbjct: 53  SLRLYPNPDAEPLKQAIARRHAADGVSVREVFVGNGSDEVLAHAFHALLQHGKPILFPDI 112

Query: 119 SFAVYALATQGLGARAIVVPAVKYGHDLDAMLAAVSDDTRLI---FVANPNNPTGTFIEG 175
           +++ Y       G   +   AV    D            + I      NPN PTG  +  
Sbjct: 113 TYSFYPTYA---GLYQVEYRAVPLAEDFTLRSEDYLGHGQAIGGIIFPNPNAPTGCLLGL 169

Query: 176 PKLEAFLDKVPRHVVVVLDEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLR 235
             +E  L   P  VVVV DEAY ++  Q     +I  V+RYPNLLV +T SK+  LAG+R
Sbjct: 170 ADVERILQGNPERVVVV-DEAYIDFGGQS----AIPLVQRYPNLLVVQTLSKSRALAGMR 224

Query: 236 VGFAIAQPELTDLLNRVRQPFNVNTL---AQAAAIAALNDKAFLEKSAALNAQGYRRLTE 292
           VGFA+   +L D L RV+  FN   L   A A A AA+ D+ +  K+  +       L  
Sbjct: 225 VGFAVGHADLIDALERVKNSFNSYPLDRPAIAGATAAIEDEDYFRKTCNMVIASRTALAA 284

Query: 293 AFDKLGLEYVPSDGNFVLVRVGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGL 352
               LG + +PS  NF+ VR    DAA  ++   L   G+IVR   +  + Q+LRITIG 
Sbjct: 285 QLAGLGFQVLPSAANFLFVRHPQHDAA--QLAAALRADGIIVRHFKSERISQFLRITIGT 342

Query: 353 PEENEAFIAALERTL 367
            E+    + AL R L
Sbjct: 343 DEDCGVLVEALRRHL 357


Lambda     K      H
   0.318    0.135    0.385 

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: 331
Number of extensions: 19
Number of successful extensions: 6
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: 370
Length of database: 360
Length adjustment: 30
Effective length of query: 340
Effective length of database: 330
Effective search space:   112200
Effective search space used:   112200
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: 49 (23.5 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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