GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aspA in Desulfovibrio vulgaris Hildenborough

Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate 207231 DVU1766 aspartate ammonia-lyase, putative

Query= BRENDA::Q9LCC6
         (468 letters)



>MicrobesOnline__882:207231
          Length = 470

 Score =  372 bits (956), Expect = e-107
 Identities = 193/462 (41%), Positives = 279/462 (60%)

Query: 5   VRIEKDFLGEKEIPKDAYYGVQTIRATENFPITGYRIHPELIKSLGIVKKSAALANMEVG 64
           +RIE D LG+  +P+ A +G  T RA  N  ++G  +HPE+I++ G VK++ A  NM +G
Sbjct: 9   IRIEHDLLGDCAVPRTALHGAHTQRALSNVALSGRPLHPEIIRAFGAVKRACARTNMNLG 68

Query: 65  LLDKEVGQYIVKAADEVIEGKWNDQFIVDPIQGGAGTSINMNANEVIANRALELMGEEKG 124
            L +EV + I+ A DE+ +G   +  +VD +QGGAGTS NMN NEV+ANRA E++G  +G
Sbjct: 69  HLSREVAEAIIMACDELEDGGLGEHIVVDALQGGAGTSANMNVNEVLANRAEEMLGGTRG 128

Query: 125 NYSKISPNSHVNMSQSTNDAFPTATHIAVLSLLNQLIETTKYMQQEFMKKADEFAGVIKM 184
            Y  + P +HVN+ QSTND FPTA  IA L LL +L      +Q  F      FA V+++
Sbjct: 129 QYQLVDPLAHVNLHQSTNDVFPTAVRIAALRLLARLEPAIAALQSAFQTHEASFAQVVRL 188

Query: 185 GRTHLQDAVPILLGQEFEAYARVIARDIERIANTRNNLYDINMGATAVGTGLNADPEYIS 244
           GRT LQDAVP+  G    A+A  ++RD  R+      L  +N+G TA+GTG+ A   YI 
Sbjct: 189 GRTQLQDAVPMTFGAACGAWAEALSRDRWRVFKCSERLRVVNLGGTAIGTGIAAPRSYIL 248

Query: 245 IVTEHLAKFSGHPLRSAQHLVDATQNTDCYTEVSSALKVCMINMSKIANDLRLMASGPRA 304
            V + L + +G PL  A++L+DATQN D + EVS  LK    N+ K+++DLRL+ASGP  
Sbjct: 249 SVVDRLREDTGLPLARAENLMDATQNVDAFVEVSGILKAHASNLLKLSSDLRLLASGPGG 308

Query: 305 GLSEIVLPARQPGSSIMPGKVNPVMPEVMNQVAFQVFGNDLTITSASEAGQFELNVMEPV 364
           G+ E+VLP  Q GSSIMPGKVNPV+ E + Q A Q   NDL IT +++ GQ ELN   P+
Sbjct: 309 GIGEVVLPPVQAGSSIMPGKVNPVVCETVAQAAMQATANDLAITLSAQHGQLELNAFMPL 368

Query: 365 LFFNLIQSISIMTNVFKSFTENCLKGIKANEERMKEYVEKSIGIITAINPHVGYETAAKL 424
           +   L+  I ++TN    F   C++G+  + E    +V  S   +TA+ P +GY  A+++
Sbjct: 369 IADALLHGIELLTNACDLFRTRCVEGLHPDTETCARHVSTSTATLTALVPEIGYAAASEM 428

Query: 425 AREAYLTGESIRELCIKYGVLTEEQLNEILNPYEMTHPGIAG 466
           AR     G  +       G++ E++L  +L+P  +   G  G
Sbjct: 429 ARHMREHGTDVFGAAKATGLIDEDRLARLLSPERLVALGYRG 470


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: 505
Number of extensions: 17
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: 470
Length adjustment: 33
Effective length of query: 435
Effective length of database: 437
Effective search space:   190095
Effective search space used:   190095
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 17 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