GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Pedobacter sp. GW460-11-11-14-LB5

Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate CA265_RS03630 CA265_RS03630 histidinol-phosphate transaminase

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



>FitnessBrowser__Pedo557:CA265_RS03630
          Length = 346

 Score =  152 bits (384), Expect = 1e-41
 Identities = 108/333 (32%), Positives = 172/333 (51%), Gaps = 23/333 (6%)

Query: 37  VKLASNENPLGMPESAQRAMAQAASELGRYPDANAFELKAALSERYGVPADWVTLGNGSN 96
           V L +NEN  G P  A            RYPD    +LK A+S+  GVP +   LGNGS+
Sbjct: 30  VFLDANENSYGSPLPAN---------YNRYPDPLQLDLKDAISKIKGVPIENTFLGNGSD 80

Query: 97  DILEIAAHAFVEKGQ-SIVYAQYSFAVYALATQGLGARAIVVPAV-KYGHDLDAMLAAVS 154
           + +++   AF   G+ +++    ++ +Y ++          V  +  +  D++ +   + 
Sbjct: 81  EAIDLLFRAFCNPGKDNVIVLPPTYGMYEVSANINDVEIRKVSLLPNFQLDMEKIAETID 140

Query: 155 DDTRLIFVANPNNPTGTFIEGPKLEAFLDKVPRHVVVVLDEAYTEYLPQEKRYDSIAWVR 214
            +T+LIF+ +PNNPTG  I    +E  L     + +VV+DEAY  Y  Q+     +    
Sbjct: 141 KNTKLIFICSPNNPTGNSINREDIETILANF--NGIVVVDEAYINYARQKTFIQELT--- 195

Query: 215 RYPNLLVSRTFSKAFGLAGLRVGFAIAQPELTDLLNRVRQPFNVNTLAQAAAIAALNDKA 274
            Y NL+V +TFSKA+GLA LR+G A +  ++ D+LN+++ P+N+N   Q  A  AL + A
Sbjct: 196 EYGNLVVLQTFSKAWGLAALRLGMAFSSTKVIDVLNKIKPPYNINQATQDLAFEALKNIA 255

Query: 275 FLEKSAALNAQGYRRLTEAFDKLGL--EYVPSDGNFVLVRVGNDDAAGNRVNLELLKQGV 332
            +      +     RL++A   L +  +  PSD NF+L  V   DA   ++   L+ QG+
Sbjct: 256 QVNDWIKESVAERDRLSKALTALNIVKKVYPSDANFILTEV--TDAL--KIYDTLVDQGI 311

Query: 333 IVRPVGNYGLPQ-WLRITIGLPEENEAFIAALE 364
           IVR      L +  LRIT+G  EEN+  +  LE
Sbjct: 312 IVRDRSKVTLCEGCLRITVGTKEENDKLLTVLE 344


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: 317
Number of extensions: 16
Number of successful extensions: 5
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: 346
Length adjustment: 29
Effective length of query: 341
Effective length of database: 317
Effective search space:   108097
Effective search space used:   108097
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.

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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