GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aspA in Dethiosulfovibrio salsuginis USBA 82

Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate WP_085544376.1 B9Y55_RS05550 class II fumarate hydratase

Query= BRENDA::Q9LCC6
         (468 letters)



>NCBI__GCF_900177735.1:WP_085544376.1
          Length = 453

 Score =  369 bits (947), Expect = e-106
 Identities = 195/455 (42%), Positives = 291/455 (63%), Gaps = 7/455 (1%)

Query: 6   RIEKDFLGEKEIPKDAYYGVQTIRATENFPITGYRIHPELIKSLGIVKKSAALANMEVGL 65
           R+E+D LGE ++P+ A +G QT R+  NFPI   ++  E+I+++G++KK+AA+ N+E+ +
Sbjct: 4   RVERDSLGEVQVPEQALWGAQTQRSLVNFPIGTEKMPSEVIEAVGMIKKAAAIVNVELKV 63

Query: 66  LDKEVGQYIVKAADEVIEGKWNDQFIVDPIQGGAGTSINMNANEVIANRALELMGEEKGN 125
           LDKE G  I +AAD+VI G  +DQF +   Q G+GT  NMN NEV+AN A +  GE    
Sbjct: 64  LDKEKGVAIARAADKVIAGDHDDQFPLSLWQTGSGTQTNMNVNEVLANLASKYSGEP--- 120

Query: 126 YSKISPNSHVNMSQSTNDAFPTATHIA-VLSLLNQLIETTKYMQQEFMKKADEFAGVIKM 184
              I PN HVN SQS+ND FPTA H+A VL++  +LI   + M     +K D +AG++K+
Sbjct: 121 ---IHPNDHVNRSQSSNDVFPTAMHLATVLAVEERLIPAMEGMAGVLGEKRDRYAGLVKI 177

Query: 185 GRTHLQDAVPILLGQEFEAYARVIARDIERIANTRNNLYDINMGATAVGTGLNADPEYIS 244
           GRTHLQDA P+ LGQE   + R+I R    I  +   L D+ +G TAVGTGLNA   +  
Sbjct: 178 GRTHLQDATPVTLGQEIGGWLRMIERCQSMIMTSVEYLKDLAIGGTAVGTGLNAPDGFGE 237

Query: 245 IVTEHLAKFSGHPLRSAQHLVDATQNTDCYTEVSSALKVCMINMSKIANDLRLMASGPRA 304
            V   L   +G   RSA     +  + D    +   LK    ++ KIAND+R +ASGPR 
Sbjct: 238 KVAVQLGDITGIDFRSAPDKFHSLTSKDELVALHGTLKALAADLMKIANDVRWLASGPRC 297

Query: 305 GLSEIVLPARQPGSSIMPGKVNPVMPEVMNQVAFQVFGNDLTITSASEAGQFELNVMEPV 364
           GL E+V+PA +PGSSIMPGKVNP   E +  ++ QV GND  +  A+  G F+LNV  PV
Sbjct: 298 GLGELVIPANEPGSSIMPGKVNPTQVEAITMISVQVMGNDAVVGIAASQGNFQLNVFMPV 357

Query: 365 LFFNLIQSISIMTNVFKSFTENCLKGIKANEERMKEYVEKSIGIITAINPHVGYETAAKL 424
           +   ++QS+ ++++   SFTE CLKG++A+EER+    ++S+ ++TA+ P +GY+TAA +
Sbjct: 358 MINAVLQSVRLLSDGINSFTERCLKGLEADEERLSSTRDRSLMLVTALAPALGYDTAASV 417

Query: 425 AREAYLTGESIRELCIKYGVLTEEQLNEILNPYEM 459
           A++A+    +++E  +  GVLT ++ ++++ P  M
Sbjct: 418 AKKAHQERTTLKEAAVSMGVLTGDEFDKLVVPERM 452


Lambda     K      H
   0.316    0.133    0.370 

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: 518
Number of extensions: 23
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: 468
Length of database: 453
Length adjustment: 33
Effective length of query: 435
Effective length of database: 420
Effective search space:   182700
Effective search space used:   182700
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 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