GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Marinobacter adhaerens HP15

Align Probable aspartate aminotransferase; AspAT; EC 2.6.1.1; Transaminase A (uncharacterized)
to candidate GFF2141 HP15_2095 aspartate aminotransferase

Query= curated2:P63499
         (429 letters)



>FitnessBrowser__Marino:GFF2141
          Length = 404

 Score =  503 bits (1296), Expect = e-147
 Identities = 248/402 (61%), Positives = 309/402 (76%), Gaps = 1/402 (0%)

Query: 28  FAQSAKLQDVLYEIRGPVHQHAARLEAEGHRILKLNIGNPAPFGFEAPDVIMRDIIQALP 87
           + +SAKL +V YEIRG V + A RLE EGHR+LKLNIGNPA F  + P+ I +D+I  + 
Sbjct: 4   YYKSAKLDNVCYEIRGVVLREARRLEEEGHRVLKLNIGNPAAFELDVPEEIQQDVIYNMH 63

Query: 88  YAQGYSDSQGILSARRAVVTRYELVPGFPRFDVDDVYLGNGVSELITMTLQALLDNGDQV 147
            AQGY +S+G+ SAR+AV+  Y    G  + D+DD++LGNGVSELI MT+QA+L+ GD+V
Sbjct: 64  QAQGYVESKGLFSARKAVM-HYCQQRGIDKVDIDDIFLGNGVSELIVMTMQAMLNTGDEV 122

Query: 148 LIPSPDYPLWTASTSLAGGTPVHYLCDETQGWQPDIADLESKITERTKALVVINPNNPTG 207
           LIP+PDYPLWTA+ +L+ G PVHY CDE Q W PDI D+  KIT RT+A+V+INPNNPTG
Sbjct: 123 LIPAPDYPLWTAAVTLSSGKPVHYRCDEQQDWFPDIDDIRKKITRRTRAIVLINPNNPTG 182

Query: 208 AVYSCEILTQMVDLARKHQLLLLADEIYDKILYDDAKHISLASIAPDMLCLTFNGLSKAY 267
           AVYS E+L Q+++LARKH L++L+DEIYDKILYD  +HIS AS+A D+L  T+NGLSK Y
Sbjct: 183 AVYSKELLEQVIELARKHNLIILSDEIYDKILYDGTQHISTASLADDVLFFTYNGLSKNY 242

Query: 268 RVAGYRAGWLAITGPKEHASSFIEGIGLLANMRLCPNVPAQHAIQVALGGHQSIEDLVLP 327
           R AGYR+GW+ ++G K  A   IEGI +L+NMRLC NVPAQ AIQ ALGG+QSI DLV P
Sbjct: 243 RAAGYRSGWMIVSGAKHRAKDLIEGIDMLSNMRLCANVPAQLAIQTALGGYQSINDLVAP 302

Query: 328 GGRLLEQRDIAWTKLNEIPGVSCVKPAGALYAFPRLDPEVYDIDDDEQLVLDLLLSEKIL 387
           GGRL EQR+ AW  LN+IPGVSCVKP GALY FP+LDP+ + I +DE+LVLDLLL EKIL
Sbjct: 303 GGRLYEQRETAWRMLNDIPGVSCVKPQGALYLFPKLDPKHFPIVNDEKLVLDLLLQEKIL 362

Query: 388 VTQGTGFNWPAPDHLRLVTLPWSRDLAAAIERLGNFLVSYRQ 429
           + QG+ FN     HLR+V LP    L  A+ RLGNFL  Y+Q
Sbjct: 363 LVQGSAFNIDDRQHLRVVFLPREDTLEDAMGRLGNFLGQYQQ 404


Lambda     K      H
   0.320    0.138    0.419 

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: 544
Number of extensions: 27
Number of successful extensions: 2
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: 429
Length of database: 404
Length adjustment: 31
Effective length of query: 398
Effective length of database: 373
Effective search space:   148454
Effective search space used:   148454
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: 50 (23.9 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