GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Streptacidiphilus oryzae TH49

Align Aspartate aminotransferase; AAT; AspAT; EC 2.6.1.1 (characterized)
to candidate WP_037575239.1 BS73_RS22570 pyridoxal phosphate-dependent aminotransferase

Query= SwissProt::Q82DR2
         (408 letters)



>NCBI__GCF_000744815.1:WP_037575239.1
          Length = 415

 Score =  697 bits (1799), Expect = 0.0
 Identities = 350/415 (84%), Positives = 382/415 (92%), Gaps = 7/415 (1%)

Query: 1   MSAATP-------PTERRVSARVGAISESATLAVDAKAKALKAAGRPVIGFGAGEPDFPT 53
           MSAA P       P +RRVSARVGAI+ESATLAVDAKAKALKAAGRPVIGFGAGEPDFPT
Sbjct: 1   MSAAAPTPDPSVRPADRRVSARVGAIAESATLAVDAKAKALKAAGRPVIGFGAGEPDFPT 60

Query: 54  PDYIVQAAIEACSNPKYHRYTPAGGLPELKAAIAAKTLRDSGYEVDASQVLVTNGGKQAI 113
           P+YIVQAA+EAC++PK HRYTPAGGLPELK AIA KTLRDSGY V+ +QVLVTNGGKQAI
Sbjct: 61  PEYIVQAAVEACTDPKNHRYTPAGGLPELKQAIADKTLRDSGYRVEPAQVLVTNGGKQAI 120

Query: 114 YEAFAAILDPGDEVIVPAPYWTTYPESIRLAGGVPVDVVADETTGYRVSVEQLEAARTEN 173
           YEAFAAILD GDEVIVPAPYWTTYPESIRLAGGVPVDVVADETTGY+V+VEQLEAARTEN
Sbjct: 121 YEAFAAILDEGDEVIVPAPYWTTYPESIRLAGGVPVDVVADETTGYKVTVEQLEAARTEN 180

Query: 174 TKVLLFVSPSNPTGAVYTREQIEEIGRWAAEKGLWVLTDEIYEHLVYGDAEFHSLPVVVP 233
           TKV+LFVSPSNPTG+VYT ++   IG+WAAE GLWVLTDEIYEHLVYGDA+F SLPV+VP
Sbjct: 181 TKVVLFVSPSNPTGSVYTEDEARAIGQWAAEHGLWVLTDEIYEHLVYGDAKFTSLPVLVP 240

Query: 234 ELADKCIVVNGVAKTYAMTGWRVGWVIGPKDVIKAATNLQSHATSNVSNVAQVAALAAVS 293
           ELA+KCIVVNGVAKTYAMTGWRVGWVIGPKDV+KAA NLQSHATSNV+NVAQ AALAAV+
Sbjct: 241 ELAEKCIVVNGVAKTYAMTGWRVGWVIGPKDVVKAAQNLQSHATSNVNNVAQRAALAAVT 300

Query: 294 GDLTAVAEMREAFDRRRKTIVRMLNEIGGVLCPEPEGAFYAYPSVKALLGKEIRGKRPQD 353
           GDL+AV EM+ AFDRRR+TIVRMLNEI G +CPEPEGAFYAYPSVK +LGKEIRGKRP+ 
Sbjct: 301 GDLSAVEEMKTAFDRRRRTIVRMLNEIPGFVCPEPEGAFYAYPSVKGVLGKEIRGKRPRT 360

Query: 354 TVELAALILEEAEVAVVPGEAFGTPGYLRLSYALGDEDLVEGVSRIQKLLSEAKD 408
           + ELA +IL+E EVAVVPGEAFGTPGYLRLSYALGD+DLVEGVSRIQKLL+EA D
Sbjct: 361 SAELAEVILDEVEVAVVPGEAFGTPGYLRLSYALGDDDLVEGVSRIQKLLAEATD 415


Lambda     K      H
   0.315    0.132    0.381 

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: 639
Number of extensions: 19
Number of successful extensions: 1
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: 408
Length of database: 415
Length adjustment: 31
Effective length of query: 377
Effective length of database: 384
Effective search space:   144768
Effective search space used:   144768
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: 42 (22.0 bits)
S2: 50 (23.9 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