GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Sphingobium czechense LL01

Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate WP_066609128.1 V473_RS20300 NAD-dependent succinate-semialdehyde dehydrogenase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_495
         (480 letters)



>NCBI__GCF_001046645.1:WP_066609128.1
          Length = 487

 Score =  565 bits (1456), Expect = e-165
 Identities = 282/474 (59%), Positives = 356/474 (75%), Gaps = 2/474 (0%)

Query: 3   LKDTQLFRQQAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALP 62
           L +  LF ++AFI GAWV A +G T+ V+NPATG I+GTVP  G A+T  AI AA+ A P
Sbjct: 5   LDNPALFIERAFIGGAWVGATSGATVPVDNPATGAIIGTVPDCGEADTLAAIAAAEAAFP 64

Query: 63  AWRALTAKERATKLRRWYELIIENQDDLARLMTLEQGKPLAEAKGEIVYAASFIEWFAEE 122
           AW+A TA +RA  L RW+ L++ N  DL R+MT EQGKP+AEA+GEI YAASFI+WFAEE
Sbjct: 65  AWKAQTAGDRAAVLERWHALVLANVADLGRIMTAEQGKPIAEAEGEIRYAASFIKWFAEE 124

Query: 123 AKRIYGDVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPA 182
            +R+ G ++P  + ++R++V+K+P+GV+AAITPWNFPAAMITRK  PALAAGC +V+KP+
Sbjct: 125 GRRVDGGIVPAPEANRRILVMKEPVGVSAAITPWNFPAAMITRKCAPALAAGCPVVVKPS 184

Query: 183 SQTPFSAFALAELAQRAGIPAGVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLM 242
             TPF+A ALA+LA+ AGIPAGVF++V+G    IG  LT++P+VRKLSFTGST +G  LM
Sbjct: 185 ELTPFTALALAKLAEEAGIPAGVFNIVTGLPTAIGGALTASPVVRKLSFTGSTRVGSLLM 244

Query: 243 SECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDGVY 302
            +CA  IK+VS ELGGNAP IVFDDAD+D AV  A++SK+RN GQTCVCANR+ +QDGVY
Sbjct: 245 RQCADTIKRVSFELGGNAPLIVFDDADVDIAVASAMVSKFRNAGQTCVCANRILVQDGVY 304

Query: 303 DAFAEKLKVAVAKLKIGNGLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVL--AGGKP 360
           D FAEKL  AV+ LK+  G   G+T GPLI+  AV KVQ H+ DALS GAT+   A    
Sbjct: 305 DQFAEKLARAVSALKVAPGDRTGSTIGPLINVAAVEKVQAHVEDALSHGATLFAQAANDA 364

Query: 361 MEGNFFEPTILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARD 420
               F  P ILT    +  +A+EETFGP+APLFRF  E + I ++N T +GLA+YFY  +
Sbjct: 365 TGARFATPVILTGATRDMRLAQEETFGPVAPLFRFTHEEEGIELANATSYGLAAYFYTEN 424

Query: 421 LGRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIK 474
           L R FRVAE LE GMV +N+G I+ EVAPFGG+K SGLGREG+  GIE+YLE K
Sbjct: 425 LHRAFRVAERLEAGMVALNSGAIAMEVAPFGGVKMSGLGREGAHAGIEEYLETK 478


Lambda     K      H
   0.317    0.135    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: 645
Number of extensions: 21
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: 480
Length of database: 487
Length adjustment: 34
Effective length of query: 446
Effective length of database: 453
Effective search space:   202038
Effective search space used:   202038
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