GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Burkholderia phytofirmans PsJN

Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate BPHYT_RS30285 BPHYT_RS30285 succinate-semialdehyde dehydrogenase

Query= SwissProt::Q9I6M5
         (483 letters)



>FitnessBrowser__BFirm:BPHYT_RS30285
          Length = 490

 Score =  542 bits (1397), Expect = e-159
 Identities = 268/481 (55%), Positives = 343/481 (71%), Gaps = 4/481 (0%)

Query: 7   KLFRQQAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKALPAWRA 66
           +L R Q  +DGAW  A +G    V NPATGE I  V   GAA+ R A +AA +A PAWR 
Sbjct: 9   ELIRPQNLIDGAWTGAADGARFAVTNPATGETIVEVADSGAADARAATDAAARAFPAWRD 68

Query: 67  LTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFGEEAKRI 126
              +ERA  LRRW  L++ N DDLA+LM++EQGKPLAEA+GE+AY AS++ WF +EA RI
Sbjct: 69  TLPRERAEILRRWHALIVANTDDLAKLMSMEQGKPLAEARGEVAYGASYVAWFADEATRI 128

Query: 127 YGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPASQTP 186
           YGD IP  Q  KR+  +K+P+GV AAITPWNFP AMI RK  PALAAGCT+V KPA  TP
Sbjct: 129 YGDLIPQQQRGKRMSAVKEPVGVIAAITPWNFPLAMIARKIAPALAAGCTVVAKPAEDTP 188

Query: 187 YSALALAELAERAGIPKGVFSVVTGSAGE---VGGELTSNPIVRKLTFTGSTEIGRQLMA 243
            +ALALA LA+ AG+P GV ++++ S  +      +  ++  VRK+TFTGST +G+ L  
Sbjct: 189 LTALALAVLAQEAGLPDGVLNMLSASREQGIAAVADWLADSRVRKITFTGSTPVGKHLAR 248

Query: 244 ECAQDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDGVYD 303
           E A  +KK+SLELGGNAPFIVFDDADLDAAV G + +K+RN GQTCVC NR+YVQ GVY+
Sbjct: 249 ESAGTLKKLSLELGGNAPFIVFDDADLDAAVTGLMAAKFRNGGQTCVCPNRVYVQAGVYE 308

Query: 304 AFVDKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKP-HA 362
            F D L   V  L +    +     GP+I+ +A+ K+  H+ DAV  GAKV+ GGK    
Sbjct: 309 RFADLLAKRVGALKVAPATDPQAQIGPMINERAIQKIARHVEDAVKHGAKVLVGGKRLTE 368

Query: 363 LGGTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYARD 422
           LG  ++ PT+L D   + LVS +ETFGP+AP+FRF +EAE I +SNDT FGLA+YFY +D
Sbjct: 369 LGPNYYAPTVLTDARDDMLVSCEETFGPVAPLFRFNEEAEAIRLSNDTPFGLAAYFYTQD 428

Query: 423 LARVFRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLGG 482
           + R+ RVA QLE G++GIN G +S+E APFGG+K SG GREGSKYG++DY+ IKY+C GG
Sbjct: 429 VRRINRVAAQLEAGVIGINEGAVSSEAAPFGGVKESGYGREGSKYGLDDYMSIKYMCQGG 488

Query: 483 I 483
           +
Sbjct: 489 L 489


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: 665
Number of extensions: 13
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: 490
Length adjustment: 34
Effective length of query: 449
Effective length of database: 456
Effective search space:   204744
Effective search space used:   204744
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