GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Cupriavidus basilensis 4G11

Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate RR42_RS24555 RR42_RS24555 succinate-semialdehyde dehydrogenase

Query= SwissProt::Q9I6M5
         (483 letters)



>FitnessBrowser__Cup4G11:RR42_RS24555
          Length = 494

 Score =  628 bits (1619), Expect = 0.0
 Identities = 305/478 (63%), Positives = 375/478 (78%)

Query: 2   QLKDAKLFRQQAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKAL 61
           +L+D  L   +A++   W +A  G++  V NPATGEI+  V  +  AE   AI A+ +A 
Sbjct: 14  RLRDPSLLETRAWLASGWQEASGGRSFAVTNPATGEILARVASLSGAEVESAITASAQAQ 73

Query: 62  PAWRALTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFGE 121
             W+  ++ ERA  LR WFDLMI N DDLA +MT EQGKPLAEA+GEI YAASF+EWF E
Sbjct: 74  AVWQRRSSHERAKLLRAWFDLMIANADDLALIMTSEQGKPLAEARGEILYAASFVEWFAE 133

Query: 122 EAKRIYGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKP 181
           EAKRIYGD  P  Q DKRI+VI+QP+GV AAITPWNFP+AMITRK  PALAAGC+++++P
Sbjct: 134 EAKRIYGDVAPHPQTDKRILVIRQPVGVCAAITPWNFPAAMITRKVAPALAAGCSIIVRP 193

Query: 182 ASQTPYSALALAELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQL 241
           A  TP +ALALA LAERAGIP GV  +V G + E+G  LT++P+VRKL+FTGSTE+GR L
Sbjct: 194 ADLTPLTALALAVLAERAGIPAGVLQMVCGPSREIGAVLTASPVVRKLSFTGSTEVGRVL 253

Query: 242 MAECAQDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDGV 301
           M++ +  IK++SLELGGNAPFIVFDDADLDAA+EGA+ SKYRN+GQTCVCANR  VQDG+
Sbjct: 254 MSQSSPTIKRLSLELGGNAPFIVFDDADLDAAIEGAMASKYRNSGQTCVCANRFLVQDGI 313

Query: 302 YDAFVDKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKPH 361
           YD FV+ L   VA+L +GNG+E GV  GPLI   A   ++  I DAV KGAKVV GGK H
Sbjct: 314 YDRFVEALVRRVAELKVGNGVEPGVQQGPLIQKSACEHLQAMIDDAVGKGAKVVVGGKGH 373

Query: 362 ALGGTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYAR 421
           ALGGTFFEPT++     +  V+++E FGP+APVFRF+DEAE IA++NDTE+GLA+Y Y R
Sbjct: 374 ALGGTFFEPTVIAGATPDMRVAREELFGPVAPVFRFRDEAEAIALANDTEYGLAAYLYTR 433

Query: 422 DLARVFRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLC 479
           D AR++RV E LEYGMVG+NTGLISNEVAPFGG+K SGLGREGS+YGI++YLEIKYLC
Sbjct: 434 DNARIWRVGEALEYGMVGLNTGLISNEVAPFGGVKQSGLGREGSRYGIDEYLEIKYLC 491


Lambda     K      H
   0.317    0.135    0.391 

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: 687
Number of extensions: 14
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: 483
Length of database: 494
Length adjustment: 34
Effective length of query: 449
Effective length of database: 460
Effective search space:   206540
Effective search space used:   206540
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 17 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