Aligments for a candidate for ilvE in Bacteroides thetaiotaomicron VPI-5482

GapMind for Amino acid biosynthesis

Aligments for a candidate for ilvE 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)



>lcl|FitnessBrowser__Btheta:350263 BT0735 aspartate decarboxylase
           AsdA (NCBI ptt file)
          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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Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis