GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Paraburkholderia bryophila 376MFSha3.1

Align NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized)
to candidate H281DRAFT_03178 H281DRAFT_03178 succinate semialdehyde dehydrogenase

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



>FitnessBrowser__Burk376:H281DRAFT_03178
          Length = 486

 Score =  675 bits (1741), Expect = 0.0
 Identities = 329/481 (68%), Positives = 390/481 (81%), Gaps = 2/481 (0%)

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

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

Query: 121 EEAKRIYGDVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVIK 180
           EE KR+ GD IP    DKR++V K+P+GV AAITPWNFPAAMITRK GPALAAGC +++K
Sbjct: 124 EEGKRLNGDTIPTPANDKRIVVTKEPVGVCAAITPWNFPAAMITRKVGPALAAGCPIIVK 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
           VYDAFA KL+AAV +L +G G E G T GPLI+E AV KV+ HI DAL KGA ++ GGK 
Sbjct: 304 VYDAFAAKLRAAVEQLTVGRGTEAGVTQGPLINEAAVLKVESHIEDALAKGARVVTGGKR 363

Query: 360 -SMEGNFFEPTILVNVPKDAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYA 418
            ++   FFEPTIL +V  D  VA++ETFGPLAPLFRF  + EVIA++NDTEFGLASYFY+
Sbjct: 364 HALGHGFFEPTILADVTPDMKVARDETFGPLAPLFRFSSDEEVIALANDTEFGLASYFYS 423

Query: 419 RDLGRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCL 478
           RD+GRV+RVAEALEYGMVG+NTGLISNEVAPFGG+K SGLGREGS YGI+DY+ IKY+C+
Sbjct: 424 RDIGRVWRVAEALEYGMVGINTGLISNEVAPFGGVKQSGLGREGSHYGIDDYVVIKYMCV 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: 720
Number of extensions: 12
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:

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