GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ans in Mesorhizobium ciceri WSM1271

Align Isoaspartyl peptidase/L-asparaginase; Asparaginase-like protein 1; Asparaginase-like sperm autoantigen; Beta-aspartyl-peptidase; Glial asparaginase; Isoaspartyl dipeptidase; L-asparagine amidohydrolase; EC 3.4.19.5; EC 3.5.1.1 (characterized)
to candidate YP_004134273.1 Mesci_6097 peptidase t2 asparaginase 2

Query= SwissProt::Q8VI04
         (333 letters)



>NCBI__GCF_000185905.1:YP_004134273.1
          Length = 300

 Score =  167 bits (422), Expect = 4e-46
 Identities = 94/227 (41%), Positives = 133/227 (58%), Gaps = 14/227 (6%)

Query: 28  VVVHGGGASNISPGRKELVSEGIAKAATEGYNILKAGGSAVDAVEGAVTMLENDPEFNAG 87
           +++HGG A  I P  +E    G  KA   G  +L  GG+AVDAVE A  +LE DP FNAG
Sbjct: 4   LILHGG-AKEIDPEEEEAHRNGCIKALEAGRAVLAGGGTAVDAVEAAGRVLETDPTFNAG 62

Query: 88  YGSVLNADGDIEMDASIMDGKDLSAGAVSAVRCIANPVKLARLVMEKTPHCFLTGRGAEK 147
           YGS LN+DG++EM A +M+G++ + GAV+ ++ + +P+ +A+ ++ + P   L   GA +
Sbjct: 63  YGSALNSDGEVEMCAGVMEGRNFNVGAVAVIKGVRHPISVAKAMLHEEP-ILLASDGARR 121

Query: 148 FAADMGIPQTPAEKLITERTKKHLEKEKLEKGAQKADCPKNSGTVGAVALDCKGNLAYAT 207
           FAAD  +       L+T + +    K + +             T+G VALD  G+LA  T
Sbjct: 122 FAADKQLELCDPADLVTPQQRDLASKSEAK------------DTIGVVALDQYGDLAVGT 169

Query: 208 STGGIVNKMVGRVGDSPCIGAGGYADNNLGAVSTTGHGESILKVNLA 254
           STGG+     GRVGDSP  G G YADN LGAV+ +G GE I +  LA
Sbjct: 170 STGGLDGSAPGRVGDSPQPGCGYYADNQLGAVAFSGDGEHIARKALA 216


Lambda     K      H
   0.313    0.131    0.379 

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: 277
Number of extensions: 15
Number of successful extensions: 2
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: 333
Length of database: 300
Length adjustment: 27
Effective length of query: 306
Effective length of database: 273
Effective search space:    83538
Effective search space used:    83538
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 48 (23.1 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