GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aspA in Caldicellulosiruptor kronotskyensis 2002

Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate WP_013431069.1 CALKRO_RS10910 aspartate ammonia-lyase

Query= BRENDA::Q9LCC6
         (468 letters)



>NCBI__GCF_000166775.1:WP_013431069.1
          Length = 461

 Score =  432 bits (1111), Expect = e-125
 Identities = 225/453 (49%), Positives = 306/453 (67%)

Query: 6   RIEKDFLGEKEIPKDAYYGVQTIRATENFPITGYRIHPELIKSLGIVKKSAALANMEVGL 65
           RIEKDFLG  E+     YG+ T RA  NF ++G  +  +LIK+  +VKK+ A+AN EVGL
Sbjct: 3   RIEKDFLGSIELSDIELYGIHTKRAFANFNVSGKSVDKDLIKAFVMVKKACAIANYEVGL 62

Query: 66  LDKEVGQYIVKAADEVIEGKWNDQFIVDPIQGGAGTSINMNANEVIANRALELMGEEKGN 125
           LD+++   IV A DE++ GK++DQFIVD  QGGAGTS NMN NEVIAN AL  +G + G 
Sbjct: 63  LDEKIKDAIVFACDEILAGKYDDQFIVDRFQGGAGTSTNMNVNEVIANVALTHIGRKPGE 122

Query: 126 YSKISPNSHVNMSQSTNDAFPTATHIAVLSLLNQLIETTKYMQQEFMKKADEFAGVIKMG 185
           Y  I P +HVNMSQSTND +PTA  IA +  + +L E    +Q+   KK  EF  VIK G
Sbjct: 123 YDIIHPINHVNMSQSTNDVYPTALRIATIWNVRELSEECAELQKSLQKKEHEFEDVIKAG 182

Query: 186 RTHLQDAVPILLGQEFEAYARVIARDIERIANTRNNLYDINMGATAVGTGLNADPEYISI 245
           RT LQDA+P+ LGQEF AYA+ I+RD  R+      L  +N+GATAVGTG+NA  +YI  
Sbjct: 183 RTQLQDALPVTLGQEFGAYAQAISRDRWRLYKVEERLRVVNLGATAVGTGVNAPLKYIFK 242

Query: 246 VTEHLAKFSGHPLRSAQHLVDATQNTDCYTEVSSALKVCMINMSKIANDLRLMASGPRAG 305
           V E L   +   L  + +L+DATQN D + E S  LK   +N+SKIANDLRL++SGP  G
Sbjct: 243 VIEILRNLTKIGLARSDYLMDATQNADVFVECSGLLKALAVNLSKIANDLRLLSSGPNTG 302

Query: 306 LSEIVLPARQPGSSIMPGKVNPVMPEVMNQVAFQVFGNDLTITSASEAGQFELNVMEPVL 365
           L+EI +PA Q GSSIMPGKVNPV+PE++N VAFQV  ND  IT A++AGQ ELN   P++
Sbjct: 303 LNEINMPAVQAGSSIMPGKVNPVIPELINTVAFQVMANDFAITLAAQAGQLELNAFLPLI 362

Query: 366 FFNLIQSISIMTNVFKSFTENCLKGIKANEERMKEYVEKSIGIITAINPHVGYETAAKLA 425
             NL++S+ I+ N  K F + C+ GI AN+E+  EY +K+  I  ++   +GY+ AA++A
Sbjct: 363 ANNLLESLKILKNGIKIFRQQCIDGITANKEKCLEYAKKTPAIAASLIDRIGYDKAAEIA 422

Query: 426 REAYLTGESIRELCIKYGVLTEEQLNEILNPYE 458
           ++A L  + I ++  +  ++ E++  E+LNP+E
Sbjct: 423 KKAILENKQIIDVVKELNIMDEKEAQELLNPFE 455


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: 582
Number of extensions: 24
Number of successful extensions: 1
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: 461
Length adjustment: 33
Effective length of query: 435
Effective length of database: 428
Effective search space:   186180
Effective search space used:   186180
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