GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aspA in Pontimonas salivibrio CL-TW6

Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate WP_104913122.1 C3B54_RS02650 class II fumarate hydratase

Query= BRENDA::Q9LCC6
         (468 letters)



>NCBI__GCF_002950575.1:WP_104913122.1
          Length = 467

 Score =  369 bits (947), Expect = e-106
 Identities = 207/467 (44%), Positives = 280/467 (59%), Gaps = 12/467 (2%)

Query: 4   DVRIEKDFLGEKEIPKDAYYGVQTIRATENFPITGYRIHPELIKSLGIVKKSAALANMEV 63
           D RIE D +GE  +PKDA Y  QT RA ENFPI+G  + P  I +L  VKK+AA AN E+
Sbjct: 7   DFRIEHDTMGEVRVPKDALYRAQTQRAVENFPISGRGLEPGHIIALAEVKKAAASANQEL 66

Query: 64  GLLDKEVGQYIVKAADEVIEGKWNDQFIVDPIQGGAGTSINMNANEVIANRALELMGEEK 123
           G+L  ++ Q I+ AADEVI G   + F VD  Q G+GTS NMN NEV+A  A     E  
Sbjct: 67  GILSADIAQAIIHAADEVISGHHLEHFPVDTYQTGSGTSSNMNMNEVLATLASRESNES- 125

Query: 124 GNYSKISPNSHVNMSQSTNDAFPTATHIAVLS-LLNQLIETTKYMQQEFMKKADEFAGVI 182
                I PN HVN SQS+ND FPT+ H+AV S L+N ++   +++ +    KA  +A V+
Sbjct: 126 -----IHPNDHVNASQSSNDVFPTSVHVAVTSALVNDVVPALEHLARALEDKAQAWATVV 180

Query: 183 KMGRTHLQDAVPILLGQEFEAYARVIARDIERIANTRNNLYDINMGATAVGTGLNADPEY 242
           K GRTHL DA P+  GQEF  YAR +   IERI +    + ++ +G TA GTG+N    +
Sbjct: 181 KPGRTHLMDATPVTFGQEFSGYARQVRLGIERIHSALPRVAEVPLGGTATGTGINTPVGF 240

Query: 243 ISIVTEHLAKFSGHPLRSAQHLVDATQNTDCYTEVSSALKVCMINMSKIANDLRLMASGP 302
              V   LA  +G PL  A    +A    D   E S AL+   ++++KIAND+R M SGP
Sbjct: 241 SERVIALLATHTGLPLTEALDHFEAQGARDGLVEASGALRTIAVSLTKIANDVRWMGSGP 300

Query: 303 RAGLSEIVLPARQPGSSIMPGKVNPVMPEVMNQVAFQVFGNDLTITSASEAGQFELNVME 362
             GL E+ LP  QPGSSIMPGKVNPV+PE +  V  +V GND T+  A  +G FELNV  
Sbjct: 301 NTGLGELALPDLQPGSSIMPGKVNPVIPEALLMVCAKVVGNDQTVAWAGASGNFELNVAI 360

Query: 363 PVLFFNLIQSISIMTNVFKSFTENCLKGIKANEERMKEYVEKSIGIITAINPHVGYETAA 422
           PV+  +L++S  ++ N  ++F +  + G++ N ER +   E S  I+T +N  +GYE AA
Sbjct: 361 PVMASSLLESTRLIANASRAFADKTVAGLEVNVERARALAESSPSIVTPLNRFIGYEAAA 420

Query: 423 KLAREAYLTGESIRELCI-----KYGVLTEEQLNEILNPYEMTHPGI 464
           K+A+ A     +IRE  I     + G L+EEQL+  L+   MT PG+
Sbjct: 421 KVAKHAVAEKITIREAVIALGFVERGELSEEQLDASLDVLSMTTPGL 467


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: 554
Number of extensions: 17
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: 467
Length adjustment: 33
Effective length of query: 435
Effective length of database: 434
Effective search space:   188790
Effective search space used:   188790
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