GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__BFirm:BPHYT_RS34305 BPHYT_RS34305
           succinate-semialdehyde dehydrogenase
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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