GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dsdA in Pseudovibrio axinellae Ad2

Align L-serine ammonia-lyase (EC 4.3.1.17); D-Serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate WP_068008542.1 PsAD2_RS16875 D-cysteine desulfhydrase family protein

Query= BRENDA::O57809
         (325 letters)



>NCBI__GCF_001623255.1:WP_068008542.1
          Length = 344

 Score =  151 bits (382), Expect = 2e-41
 Identities = 105/333 (31%), Positives = 167/333 (50%), Gaps = 18/333 (5%)

Query: 5   IFALLAKFPRVELIPWETPIQYLPNISREIGAD-VYIKRDDLTGLGIGGNKIRKLEYLLG 63
           + + L +FP V L    TP++ L N+S+ +G   ++ KR+D+TG G+GGNK+RKL+ +L 
Sbjct: 6   LLSRLERFPTVGLCDLPTPLRPLKNLSQHLGGPMIWEKREDVTGQGMGGNKLRKLDRVLH 65

Query: 64  DALSKGADVVITVGAVHSNHAFVTGLAAKKLGLDAILVL--------RGKEELKGNYLLD 115
            A+  GAD +++ G V SN       AA  LGLD  L +          +    GN LL+
Sbjct: 66  RAVQDGADTLVSGGVVQSNSQRQVAAAAAILGLDCHLAVYHGRVTPPTAQYNTSGNALLN 125

Query: 116 KIMGIETRVYDAKDSFELMKYAEEIAEELKREGRKPYVIPPGGASPIGTLGYVRAVGEIA 175
            + G    ++    + +     + +A+EL  EG++P+V+P G +  +G +GY  A+ EIA
Sbjct: 126 HLYG--ATLHPKTWTGDRNGPVQALAQELLAEGKRPFVVPYGVSDALGAVGYSSAIAEIA 183

Query: 176 TQSEVKF---DSIVVAAGSGGTLAGLSLGLSILNEDIRPVGIAVGRFGEVMTSKLDNLIK 232
            QS        S+V   GSG T AGL++G      D + VGI +    E +   +     
Sbjct: 184 AQSAQNGFTPTSVVHCTGSGATQAGLAMGAQSALPDCKIVGIDIDAEPERVKGDVIEYAI 243

Query: 233 EAAELLGVKVEVR--PELYDYSFGEYGKITGEVAQIIRKVGTREGIILDPVYTGKAFYGL 290
             A LLG+  +      +  ++   YG         ++  G  E + LDPVY+ K   GL
Sbjct: 244 GGAALLGIPFDASQIEVIAGHAGPAYGIPNDATIHALQIAGRFEALTLDPVYSAKGMAGL 303

Query: 291 VDLARKG--ELGEKILFIHTGGISGTFHYGDKL 321
           + L R G  +  + ++F++TGG    F Y D L
Sbjct: 304 IALIRTGHWKNDDNVIFLNTGGTPSLFAYADAL 336


Lambda     K      H
   0.319    0.142    0.402 

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: 287
Number of extensions: 20
Number of successful extensions: 6
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: 325
Length of database: 344
Length adjustment: 28
Effective length of query: 297
Effective length of database: 316
Effective search space:    93852
Effective search space used:    93852
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 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