GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Sphingobium czechense LL01

Align succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] (characterized)
to candidate WP_066609128.1 V473_RS20300 NAD-dependent succinate-semialdehyde dehydrogenase

Query= reanno::MR1:200453
         (482 letters)



>NCBI__GCF_001046645.1:WP_066609128.1
          Length = 487

 Score =  579 bits (1492), Expect = e-170
 Identities = 289/476 (60%), Positives = 362/476 (76%)

Query: 1   MLLNDPSLLRQQCYINGQWCDANSKETVAITNPATGAVIACVPVMGQAETQAAIAAAEAA 60
           ++L++P+L  ++ +I G W  A S  TV + NPATGA+I  VP  G+A+T AAIAAAEAA
Sbjct: 3   LILDNPALFIERAFIGGAWVGATSGATVPVDNPATGAIIGTVPDCGEADTLAAIAAAEAA 62

Query: 61  LPAWRALTAKERGAKLRRWFELLNENSDDLALLMTSEQGKPLTEAKGEVTYAASFIEWFA 120
            PAW+A TA +R A L RW  L+  N  DL  +MT+EQGKP+ EA+GE+ YAASFI+WFA
Sbjct: 63  FPAWKAQTAGDRAAVLERWHALVLANVADLGRIMTAEQGKPIAEAEGEIRYAASFIKWFA 122

Query: 121 EEAKRIYGDTIPGHQGDKRIMVIKQPVGVTAAITPWNFPAAMITRKAAPALAAGCTMVVK 180
           EE +R+ G  +P  + ++RI+V+K+PVGV+AAITPWNFPAAMITRK APALAAGC +VVK
Sbjct: 123 EEGRRVDGGIVPAPEANRRILVMKEPVGVSAAITPWNFPAAMITRKCAPALAAGCPVVVK 182

Query: 181 PAPQTPFTALALAVLAERAGIPAGVFSVITGDAIAIGNEMCTNPIVRKLSFTGSTNVGIK 240
           P+  TPFTALALA LAE AGIPAGVF+++TG   AIG  +  +P+VRKLSFTGST VG  
Sbjct: 183 PSELTPFTALALAKLAEEAGIPAGVFNIVTGLPTAIGGALTASPVVRKLSFTGSTRVGSL 242

Query: 241 LMAQCAPTLKKLSLELGGNAPFIVFDDANIDAAVEGAMIAKYRNAGQTCVCANRIYVQAG 300
           LM QCA T+K++S ELGGNAP IVFDDA++D AV  AM++K+RNAGQTCVCANRI VQ G
Sbjct: 243 LMRQCADTIKRVSFELGGNAPLIVFDDADVDIAVASAMVSKFRNAGQTCVCANRILVQDG 302

Query: 301 VYDEFAEKLSMAVAKLKVGEGIIAGVTTGPLINAAAVEKVQSHLEDAIKKGATVLAGGKV 360
           VYD+FAEKL+ AV+ LKV  G   G T GPLIN AAVEKVQ+H+EDA+  GAT+ A    
Sbjct: 303 VYDQFAEKLARAVSALKVAPGDRTGSTIGPLINVAAVEKVQAHVEDALSHGATLFAQAAN 362

Query: 361 HELGGNFFEPTVLTNADKSMRVAREETFGPLAPLFKFNDVDDVIKQANDTEFGLAAYFYG 420
              G  F  P +LT A + MR+A+EETFGP+APLF+F   ++ I+ AN T +GLAAYFY 
Sbjct: 363 DATGARFATPVILTGATRDMRLAQEETFGPVAPLFRFTHEEEGIELANATSYGLAAYFYT 422

Query: 421 RDISLVWKVAESLEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKYGIEEYLEIK 476
            ++   ++VAE LE GMV +N+G I+ EVAPFGG+K SGLGREG+  GIEEYLE K
Sbjct: 423 ENLHRAFRVAERLEAGMVALNSGAIAMEVAPFGGVKMSGLGREGAHAGIEEYLETK 478


Lambda     K      H
   0.318    0.133    0.390 

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: 668
Number of extensions: 23
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: 482
Length of database: 487
Length adjustment: 34
Effective length of query: 448
Effective length of database: 453
Effective search space:   202944
Effective search space used:   202944
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 (21.7 bits)
S2: 52 (24.6 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