Align Bifunctional aspartate aminotransferase and L-aspartate beta-decarboxylase; Aspartate 4-decarboxylase; Asd; AsdP; EC 2.6.1.1; EC 4.1.1.12 (characterized)
to candidate 350263 BT0735 aspartate decarboxylase AsdA (NCBI ptt file)
Query= SwissProt::Q53IZ1 (531 letters) >FitnessBrowser__Btheta:350263 Length = 557 Score = 463 bits (1192), Expect = e-135 Identities = 240/526 (45%), Positives = 338/526 (64%), Gaps = 9/526 (1%) Query: 6 RSLANLSPFELKDELIKVASGKANRL---MLNAGRGNPNFLATTPRRAFFRLGLFAAAES 62 + + +SPFELK++LI++A ++ MLNAGRGNPN++AT PR AFF LG F E Sbjct: 31 KKMETISPFELKNKLIEMADESIKKMAHTMLNAGRGNPNWIATEPREAFFLLGKFGLCEC 90 Query: 63 ELSYSYMTVGVGGLAKLDGIEGRFERFIAEHRDQEGVKFLGKSLSYVRDQLGLDPAAFLH 122 S + G+ G+ + +GI RFE F+ E+ + G + L ++ +Y+ + DP +H Sbjct: 91 RRVQS-LEEGIAGIPQQEGIAARFEAFLKENEKEAGARLLKETYNYMLMEHAADPDRLVH 149 Query: 123 EMVDGILGCNYPVPPRMLTVSEQIVRQYIVREMAGGAVPPESVDLFAVEGGTAAMAYIFE 182 E + ++G YPVP R+L +E IV+ Y+ +EM P + DLFA EGGTAAM Y+F+ Sbjct: 150 EWAESVIGDQYPVPDRILHFTELIVQDYLAQEMCDRRPPKGTFDLFATEGGTAAMCYVFD 209 Query: 183 SLRISGLLKAGDKVAIGMPVFTPYIEIPELAQYDLKEVPIHAD---PD--NGWQYSDAEL 237 SL+ + LL GD +A+ +PVFTPYIEIPEL +Y I AD PD + WQY D ++ Sbjct: 210 SLQENFLLNQGDSIALMIPVFTPYIEIPELRRYQFDVTEISADQMTPDGLHTWQYKDEDI 269 Query: 238 DKLKDPDVKIFFCVNPSNPPSVKMDQRSLDRVRAIVAEQRPDLLILTDDVYGTFADEFQS 297 DKLK+P +K F NPSNPPS + + R+ IV P+L+I+TDDVYGTF F+S Sbjct: 270 DKLKNPQIKALFITNPSNPPSYALSPETAARIVNIVKNDNPNLMIITDDVYGTFIPHFRS 329 Query: 298 LFSVCPRNTLLVYSFSKYFGATGWRLGVIAAHKDNVFDHALSQLPESAKKALDHRYRSLL 357 L + P NTL VYSFSKYFGATGWR VIA H+DN++D +++L E L+ RY SL Sbjct: 330 LMAELPHNTLCVYSFSKYFGATGWRNAVIALHEDNIYDKMIARLSEEQTAILNKRYASLS 389 Query: 358 PDVRSLKFIDRLVADSRVVALNHTAGLSTPQQVQMVLFSLFALMDEADAYKQALKQLIRR 417 +KFIDR+VADSR +ALNHTAGLS PQQ+QM LF+ F+L+D+ D YK ++++I R Sbjct: 390 LHPEKMKFIDRMVADSRQIALNHTAGLSLPQQMQMSLFAAFSLLDKEDRYKAKMQEIIHR 449 Query: 418 REATLYRELGMPPLENPNSVNYYTLIDLQNVTCRLYGEAFSQWAVQQSSTGDMLFRVADE 477 R L+ G +E+P YY+ ID+ + YG+ F+ + + + D++FR+A+E Sbjct: 450 RLHALWDSTGFTLIEDPLRAGYYSEIDMLVWAKKFYGDEFADYLQKTYNPLDVVFRLANE 509 Query: 478 TGIVLLPGRGFGSDRPSGRASLANLNEYEYAAIGRALRRLADELYE 523 T +VLL G GF + S R SLANLNE +Y IG++++R+ DE E Sbjct: 510 TSLVLLNGGGFAGPKWSVRVSLANLNEADYVKIGQSIKRVLDEYAE 555 Lambda K H 0.321 0.138 0.400 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: 720 Number of extensions: 27 Number of successful extensions: 4 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: 531 Length of database: 557 Length adjustment: 35 Effective length of query: 496 Effective length of database: 522 Effective search space: 258912 Effective search space used: 258912 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: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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:
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