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_RS34305 BPHYT_RS34305 succinate-semialdehyde dehydrogenase

Query= SwissProt::Q9I6M5
         (483 letters)



>FitnessBrowser__BFirm:BPHYT_RS34305
          Length = 479

 Score =  628 bits (1619), Expect = 0.0
 Identities = 299/477 (62%), Positives = 374/477 (78%), Gaps = 2/477 (0%)

Query: 7   KLFRQQAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKALPAWRA 66
           +  R   ++ G W +     T  V NPATGE++  V K GAAET +AI AA++A PAWRA
Sbjct: 3   EFLRTGHFIGGEWYEG--ADTYAVLNPATGEVVAHVAKGGAAETAQAIAAAERAFPAWRA 60

Query: 67  LTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFGEEAKRI 126
           LTAKER+ +++RW +LM+EN+D LA L+T+EQGKPLAEA+GE+ YAASF EWF EEAKR 
Sbjct: 61  LTAKERSARVKRWGELMLENRDALAELLTLEQGKPLAEARGEVGYAASFFEWFAEEAKRA 120

Query: 127 YGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPASQTP 186
           YGD IP   P+ +IIV ++P+GV AAITPWNFP AMITRKAGPALAAGCTMVLKP+ +TP
Sbjct: 121 YGDVIPSPNPNAKIIVTREPVGVVAAITPWNFPLAMITRKAGPALAAGCTMVLKPSEETP 180

Query: 187 YSALALAELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQLMAECA 246
            SA ALA LA +AGIP GVF++V+G A  +GG LT + +VRKL+FTGST +G+ L  + A
Sbjct: 181 LSAFALAVLAAKAGIPPGVFNIVSGDAVAIGGALTESDVVRKLSFTGSTRVGKLLAKQSA 240

Query: 247 QDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDGVYDAFV 306
             +KK+SLELGGNAPFIVFDDADLDAAV+GA+ SK+RN GQTCVC NR YVQDG+YDAF 
Sbjct: 241 DTLKKLSLELGGNAPFIVFDDADLDAAVQGAMASKFRNTGQTCVCVNRFYVQDGIYDAFT 300

Query: 307 DKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKPHALGGT 366
             L  AV K+ +GN L+  V  GPLI+  A+ KVE H+ADA+ KGAK+++GGKPH LGGT
Sbjct: 301 SALTQAVRKMRVGNALQGEVEQGPLINQAALKKVETHVADALQKGAKILTGGKPHTLGGT 360

Query: 367 FFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYARDLARV 426
           F+EPT+L D   + L++ +ETFGP+A  FRFK EAE I  +NDT FGL++YFY RDLAR 
Sbjct: 361 FYEPTVLADADNSMLIAGEETFGPVAACFRFKTEAEAIEAANDTPFGLSAYFYTRDLARA 420

Query: 427 FRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLGGI 483
           +RV E LE GMVGIN G++S EVAPFGG+K SGLGREGSKYG+++Y E+KY+ +GG+
Sbjct: 421 WRVGEALESGMVGINEGIVSTEVAPFGGVKQSGLGREGSKYGLDEYTELKYMMMGGL 477


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: 676
Number of extensions: 10
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: 479
Length adjustment: 34
Effective length of query: 449
Effective length of database: 445
Effective search space:   199805
Effective search space used:   199805
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: 51 (24.3 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