GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gabD in Burkholderia phytofirmans PsJN

Align NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized)
to candidate BPHYT_RS22430 BPHYT_RS22430 succinate-semialdehyde dehydrogenase

Query= metacyc::MONOMER-15736
         (480 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS22430 BPHYT_RS22430
           succinate-semialdehyde dehydrogenase
          Length = 486

 Score =  676 bits (1744), Expect = 0.0
 Identities = 328/481 (68%), Positives = 389/481 (80%), Gaps = 2/481 (0%)

Query: 1   MQLKDAQLFRQQAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKA 60
           + LKD  L +  A+I G W  AD+G T +V NPATGE + TVP+MG AETRRAI+ A+ A
Sbjct: 4   LSLKDPSLLKSHAYIAGEWQGADDGTTFEVKNPATGETIATVPRMGTAETRRAIDTANAA 63

Query: 61  LPAWRALTAKERATKLRRWYELLIENQDDLGRLMTLEQGKPLAEAKGEIAYAASFIEWFA 120
            PAWRA TAK+RA  LR+W++L++EN DDL +++T EQGKPLAEAKGEI YAASF+EWFA
Sbjct: 64  WPAWRATTAKQRAVILRKWHDLMMENADDLAKILTTEQGKPLAEAKGEIQYAASFLEWFA 123

Query: 121 EEAKRIYGDVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVIK 180
           EE KR+ GD IP    DKR++V K+PIGV AAITPWNFPAAMITRK GPALAAGC +++K
Sbjct: 124 EEGKRVNGDTIPTPASDKRIVVTKEPIGVCAAITPWNFPAAMITRKVGPALAAGCPIIVK 183

Query: 181 PASQTPFSALALVELAHRAGIPKGVLSVVTGSAGDIGGELTSNPIVRKLSFTGSTEIGRQ 240
           PA  TP SALAL  LA RAG+P+GV +VVTG    IG E+T NPIVRKLSFTGST +GR 
Sbjct: 184 PAEATPLSALALAVLAERAGVPRGVFNVVTGEPKAIGAEMTGNPIVRKLSFTGSTPVGRL 243

Query: 241 LMAECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDS 300
           LMA+CA  +KKVSLELGGNAPFIVFDDADLD AV GAI SKYRN+GQTCVC NR Y+ D 
Sbjct: 244 LMAQCAPTVKKVSLELGGNAPFIVFDDADLDAAVAGAIASKYRNSGQTCVCTNRFYVHDK 303

Query: 301 VYDAFAEKLKAAVAKLKIGNGLEEGTTTGPLIDEKAVAKVQEHIADALKKGATLLAGGK- 359
           VYDAFAEKL+ AV +LK+G G E+G T GPLI++ AV KV+ HI DAL KGA ++ GGK 
Sbjct: 304 VYDAFAEKLRVAVEQLKVGRGTEDGVTQGPLINDAAVLKVESHIEDALAKGARIVTGGKR 363

Query: 360 -SMEGNFFEPTILVNVPKDAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYA 418
            ++   FFEPT+L +V     VA++ETFGPLAPLFRF  + EVI ++NDTEFGLASYFY+
Sbjct: 364 HALGHGFFEPTVLADVTPAMKVARDETFGPLAPLFRFSSDEEVIRLANDTEFGLASYFYS 423

Query: 419 RDLGRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCL 478
           RD+GRV+RVAEALEYGMVG+NTGLISNEVAPFGG+K SGLGREGS YGI+DY+ IKYLC+
Sbjct: 424 RDIGRVWRVAEALEYGMVGINTGLISNEVAPFGGVKQSGLGREGSHYGIDDYVVIKYLCV 483

Query: 479 G 479
           G
Sbjct: 484 G 484


Lambda     K      H
   0.317    0.135    0.390 

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: 717
Number of extensions: 13
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: 480
Length of database: 486
Length adjustment: 34
Effective length of query: 446
Effective length of database: 452
Effective search space:   201592
Effective search space used:   201592
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 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