GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Caulobacter crescentus NA1000

Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate CCNA_03242 CCNA_03242 succinic semialdehyde dehydrogenase

Query= SwissProt::Q9I6M5
         (483 letters)



>FitnessBrowser__Caulo:CCNA_03242
          Length = 485

 Score =  569 bits (1466), Expect = e-167
 Identities = 286/477 (59%), Positives = 356/477 (74%), Gaps = 3/477 (0%)

Query: 8   LFRQQAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKALPAWRAL 67
           L    A +DG WV  +   +  V NPA G +I +V  +GAAET  AI+AA +ALPAW A 
Sbjct: 9   LVETAALIDGQWVRGE--ASFDVLNPADGTLIAAVADLGAAETTLAIDAAHRALPAWAAR 66

Query: 68  TAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFGEEAKRIY 127
           TAKER   LRRW DL++ + DDLARLMT EQGKPLAEAKGE+ Y ASF++WF EEAKR Y
Sbjct: 67  TAKERGAILRRWSDLILAHADDLARLMTDEQGKPLAEAKGEVVYGASFIDWFAEEAKRAY 126

Query: 128 GDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPASQTPY 187
           G TIP   P KR+  IKQP+GV AAI PWNFP AMITRK GPALAAGCT+V+KPA++TP 
Sbjct: 127 GHTIPTPMPGKRLASIKQPVGVCAAIAPWNFPIAMITRKVGPALAAGCTVVVKPAAETPL 186

Query: 188 SALALAELAERAGIPKGVFSVVTGS-AGEVGGELTSNPIVRKLTFTGSTEIGRQLMAECA 246
           SALA+A LA  AG+P GV ++VT + + EVG  L  +  VRKL+FTGST IG+ L  +CA
Sbjct: 187 SALAIARLATEAGVPAGVLNIVTTTRSSEVGKVLCDDSRVRKLSFTGSTPIGKVLYQQCA 246

Query: 247 QDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDGVYDAFV 306
             +KK+SLELGGNAPFIVFDDADL+AAV+GA+ SKYRN GQTCVCANRL VQ G++DAF 
Sbjct: 247 GTMKKLSLELGGNAPFIVFDDADLEAAVDGAIASKYRNAGQTCVCANRLIVQSGIHDAFA 306

Query: 307 DKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKPHALGGT 366
            +L   VA L +G G   GV  GPLI+ KA+ KV   ++ AV  GA+V++GG  H LGG 
Sbjct: 307 ARLAEKVAALKVGPGTGEGVQIGPLINEKALTKVVGLVSGAVQAGAEVLTGGDVHGLGGH 366

Query: 367 FFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYARDLARV 426
           F++PT+LV       + ++E FGP+AP+ +F+ EAE + ++N T FGLA+YFY+RD+ R 
Sbjct: 367 FYQPTVLVGATPEMRIFQEEIFGPVAPIVKFETEAEAVELANATPFGLAAYFYSRDVGRC 426

Query: 427 FRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLGGI 483
           +RVAEQ+E GMVGIN GLIS EVAPFGG+K SGLGREG+  G+++YLE KYLC GG+
Sbjct: 427 WRVAEQIEAGMVGINEGLISTEVAPFGGVKESGLGREGASEGLDEYLETKYLCFGGV 483


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: 662
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: 483
Length of database: 485
Length adjustment: 34
Effective length of query: 449
Effective length of database: 451
Effective search space:   202499
Effective search space used:   202499
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