GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Bacteroides thetaiotaomicron VPI-5482

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.

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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