GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Rhodobacter viridis JA737

Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate WP_110805439.1 C8J30_RS08590 betaine-aldehyde dehydrogenase

Query= SwissProt::Q9I6M5
         (483 letters)



>NCBI__GCF_003217355.1:WP_110805439.1
          Length = 483

 Score =  318 bits (816), Expect = 2e-91
 Identities = 183/469 (39%), Positives = 268/469 (57%), Gaps = 4/469 (0%)

Query: 14  YVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKALPAWRALTAKERA 73
           +V+G WV+   G  I+V  P TGE+I  + +   A    A+  A  A  AW AL   ERA
Sbjct: 10  FVNGNWVEDAAGAEIEVIFPGTGEVIAILHEATPAVIEEALAGAQAAQRAWAALKPVERA 69

Query: 74  NKLRRWFDLMIENQDDLARLMTIEQGKPLAEAK-GEIAYAASFLEWFGEEAKRIYGDTIP 132
             LRR  DL+   + +LA L T++ GKP+ E    +    A  LE+F   A  + G+TIP
Sbjct: 70  RILRRAADLIRARRAELALLETLDTGKPIQETSVADWPSGADSLEYFAGLAPTLTGETIP 129

Query: 133 GHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPASQTPYSALAL 192
                     I++P+GV   I  WN+PS +   KA PAL+ G  M+ KP+  TP  AL L
Sbjct: 130 --LGGDFAYTIREPLGVCVGIGAWNYPSQIACWKAAPALSTGNAMIFKPSEITPLGALQL 187

Query: 193 AELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQLMAECAQDIKKV 252
           A +   AG+P GVF+VV G  G VGG L ++  V K++ TGS   G ++ A     +K V
Sbjct: 188 AAIFVEAGMPAGVFNVVQGR-GAVGGRLATDSRVAKVSLTGSVPTGAKVYAAAGAGMKHV 246

Query: 253 SLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDGVYDAFVDKLKAA 312
           ++ELGG +P IVF+DADL++A+  A++  + ++GQ C    R++V   + + F+ +L   
Sbjct: 247 TMELGGKSPLIVFEDADLESAIGAAMLGNFYSSGQICSNGTRVFVHKAIKERFLTRLAER 306

Query: 313 VAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKPHALGGTFFEPTI 372
            A +  G+ L+     GPL+ A   AKV  +IA A S+GA++V GG   A G  F +PT+
Sbjct: 307 TAAIKAGDPLDETTQFGPLVSAAQHAKVLGYIATAKSEGARLVCGGAAGAEGALFVQPTV 366

Query: 373 LVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYARDLARVFRVAEQ 432
             DV  +  ++++E FGP+  V  F+ E EVIA +N T+FGLA+  +  DLAR  RV  Q
Sbjct: 367 FADVTDSMTIAREEVFGPVMAVLDFETEDEVIARANGTDFGLAAGVFTADLARGHRVIAQ 426

Query: 433 LEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLG 481
           L+ G   IN   ++    PFG +K+SG+GRE SK  IE Y ++K + +G
Sbjct: 427 LQAGTTWINAYNLTPVEMPFGAVKSSGVGRENSKAAIEHYTQVKAVYVG 475


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: 600
Number of extensions: 27
Number of successful extensions: 3
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: 483
Length adjustment: 34
Effective length of query: 449
Effective length of database: 449
Effective search space:   201601
Effective search space used:   201601
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