Align aspartate 4-decarboxylase (EC 4.1.1.12) (characterized)
to candidate 350263 BT0735 aspartate decarboxylase AsdA (NCBI ptt file)
Query= BRENDA::Q93QX0 (533 letters) >FitnessBrowser__Btheta:350263 Length = 557 Score = 467 bits (1201), Expect = e-136 Identities = 243/528 (46%), Positives = 339/528 (64%), Gaps = 11/528 (2%) Query: 6 QSLAKLSPFELKDELIKIASSDGNRL---MLNAGRGNPNFLATTPRRAFFRLGLFAAAES 62 + + +SPFELK++LI++A ++ MLNAGRGNPN++AT PR AFF LG F E Sbjct: 31 KKMETISPFELKNKLIEMADESIKKMAHTMLNAGRGNPNWIATEPREAFFLLGKFGLCEC 90 Query: 63 ELSYSYMTTVGVGGLAKIDGIEGRFERYIAENRDQEGVRFLGKSLSYVRDQLGLDPAAFL 122 S G+ G+ + +GI RFE ++ EN + G R L ++ +Y+ + DP + Sbjct: 91 RRVQSLEE--GIAGIPQQEGIAARFEAFLKENEKEAGARLLKETYNYMLMEHAADPDRLV 148 Query: 123 HEMVDGILGCNYPVPPRMLNISEKIVRQYIIREMGADAIPSESVNLFAVEGGTAAMAYIF 182 HE + ++G YPVP R+L+ +E IV+ Y+ +EM P + +LFA EGGTAAM Y+F Sbjct: 149 HEWAESVIGDQYPVPDRILHFTELIVQDYLAQEMCDRRPPKGTFDLFATEGGTAAMCYVF 208 Query: 183 ESLKLNGLLKAGDKVAIGMPVFTPYIEIPELAQYALEEVAINADPSL-----NWQYPDSE 237 +SL+ N LL GD +A+ +PVFTPYIEIPEL +Y + I+AD WQY D + Sbjct: 209 DSLQENFLLNQGDSIALMIPVFTPYIEIPELRRYQFDVTEISADQMTPDGLHTWQYKDED 268 Query: 238 LDKLKDPAIKIFFCVNPSNPPSVKMDQRSLERVRNIVAEHRPDLMILTDDVYGTFADDFQ 297 +DKLK+P IK F NPSNPPS + + R+ NIV P+LMI+TDDVYGTF F+ Sbjct: 269 IDKLKNPQIKALFITNPSNPPSYALSPETAARIVNIVKNDNPNLMIITDDVYGTFIPHFR 328 Query: 298 SLFAICPENTLLVYSFSKYFGATGWRLGVVAAHQQNVFDLALDKLQESEKVALDHRYRSL 357 SL A P NTL VYSFSKYFGATGWR V+A H+ N++D + +L E + L+ RY SL Sbjct: 329 SLMAELPHNTLCVYSFSKYFGATGWRNAVIALHEDNIYDKMIARLSEEQTAILNKRYASL 388 Query: 358 LPDVRSLKFIDRLVADSRAVALNHTAGLSTPQQVQMALFSLFALMDEADEYKHTLKQLIR 417 +KFIDR+VADSR +ALNHTAGLS PQQ+QM+LF+ F+L+D+ D YK ++++I Sbjct: 389 SLHPEKMKFIDRMVADSRQIALNHTAGLSLPQQMQMSLFAAFSLLDKEDRYKAKMQEIIH 448 Query: 418 RRETTLYRELGMPPLRDENAVDYYTLIDLQDVTAKLYGEAFSEWAVKQSSTGDMLFRIAD 477 RR L+ G + D YY+ ID+ K YG+ F+++ K + D++FR+A+ Sbjct: 449 RRLHALWDSTGFTLIEDPLRAGYYSEIDMLVWAKKFYGDEFADYLQKTYNPLDVVFRLAN 508 Query: 478 ETGIVLLPGRGFGSNRPSGRASLANLNEYEYAAIGRALRKMADELYAE 525 ET +VLL G GF + S R SLANLNE +Y IG++++++ DE YAE Sbjct: 509 ETSLVLLNGGGFAGPKWSVRVSLANLNEADYVKIGQSIKRVLDE-YAE 555 Lambda K H 0.320 0.137 0.392 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: 740 Number of extensions: 29 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: 533 Length of database: 557 Length adjustment: 35 Effective length of query: 498 Effective length of database: 522 Effective search space: 259956 Effective search space used: 259956 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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