GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aspA in Sporolactobacillus vineae SL153

Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate WP_010630565.1 RH97_RS01575 aspartate ammonia-lyase

Query= BRENDA::Q9LCC6
         (468 letters)



>NCBI__GCF_000246965.1:WP_010630565.1
          Length = 466

 Score =  407 bits (1046), Expect = e-118
 Identities = 211/457 (46%), Positives = 293/457 (64%), Gaps = 1/457 (0%)

Query: 5   VRIEKDFLGEKEIPKDAYYGVQTIRATENFPITGYRIHPELIKSLGIVKKSAALANMEVG 64
           +RIE D +G KE+P  AYYG+  +RA ENF +T   I PELI  L I+KK+AA  N + G
Sbjct: 1   MRIETDAIGTKEVPSSAYYGIHALRAKENFNVTSETIDPELIDGLAIIKKAAASVNRKDG 60

Query: 65  LLDKEVGQYIVKAADEVIEGKWNDQFIVDPIQGGAGTSINMNANEVIANRALELMGEEKG 124
            L KE    I +A DEV+E K +  FIV  IQG AGTSINMNANEVIANRA+EL+G EKG
Sbjct: 61  SLSKEKAAAIRRACDEVLERKLDHAFIVPSIQGSAGTSINMNANEVIANRAIELLGGEKG 120

Query: 125 NYSKISPNSHVNMSQSTNDAFPTATHIAVLSLLNQLIETTKYMQQEFMKKADEFAGVIKM 184
           +YS I PN  VN  QSTND FP+A  +A+L L  QL            +KA E   ++K+
Sbjct: 121 SYSIIHPNDDVNRGQSTNDTFPSAGKLALLRLSRQLTLEIDRFIDSLDQKASELKDIVKI 180

Query: 185 GRTHLQDAVPILLGQEFEAYARVIARDIERIANTRNNLYDINMGATAVGTGLNADPEYIS 244
           GRT LQDA+P  +G  F+AYA    R+++ I ++R+ L  +N+G TA+GT +NA   Y+ 
Sbjct: 181 GRTQLQDALPTTVGDTFKAYAAAAGRNLDEINHSRHGLKTLNLGGTAIGTSVNASEYYVR 240

Query: 245 IVTEHLAKFSGHPLRSAQHLVDATQNTDCYTEVSSALKVCMINMSKIANDLRLMASGPRA 304
            +   ++K  G  L  A +L+DATQN D +  +S A K+  + +SK+A+DLRL++SGP+ 
Sbjct: 241 HIVPEVSKLFGEELSQADNLIDATQNVDAFVRLSHAYKLFAVTLSKMASDLRLLSSGPQF 300

Query: 305 GLSEIVLPARQPGSSIMPGKVNPVMPEVMNQVAFQVFGNDLTITSASEAGQFELNVMEPV 364
           G +E+ LP +Q GSSIMPGKVNPV+PE++NQVAFQ+ G D TIT A+EAGQ ELN  EP+
Sbjct: 301 GFNELFLPKKQAGSSIMPGKVNPVIPELVNQVAFQIMGYDTTITLAAEAGQLELNAFEPI 360

Query: 365 LFFNLIQSISIMTNVFKSFTENCLKGIKANEERMKEYVEKSIGIITAINPHVGYETAAKL 424
           +  NLI +  +++    +F  NC+ GI+AN  R  +       + TA+ P++GY     L
Sbjct: 361 IVRNLIVTSRLLSKTLVTFRINCINGIEANRPRCTDEANHCAILATALTPYIGYSKTCTL 420

Query: 425 AREAYLTGESIRELCIKYGVLTEEQLNEILNPYEMTH 461
            +E+  TG  I+ L  +   + E  L ++L+P  + H
Sbjct: 421 VKESLQTGTPIQTLAGQLPDVPESVL-KLLDPKNLIH 456


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: 547
Number of extensions: 16
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: 466
Length adjustment: 33
Effective length of query: 435
Effective length of database: 433
Effective search space:   188355
Effective search space used:   188355
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