GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Magnetospirillum magneticum AMB-1

Align succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized)
to candidate WP_011383730.1 AMB_RS06710 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::P25526
         (482 letters)



>NCBI__GCF_000009985.1:WP_011383730.1
          Length = 485

 Score =  667 bits (1720), Expect = 0.0
 Identities = 327/482 (67%), Positives = 387/482 (80%), Gaps = 1/482 (0%)

Query: 1   MKLNDSNLFRQQALINGEWLDANNGEAIDVTNPANGDKLGSVPKMGADETRAAIDAANRA 60
           + L+DS L R  A ING W+ A +GE + VTNPA+G  +  VP MGA ETR AI+AA+RA
Sbjct: 2   LDLSDSALLRDHAYINGSWVAAQSGERLAVTNPADGSLIIRVPAMGAAETRQAIEAADRA 61

Query: 61  LPAWRALTAKERATILRNWFNLMMEHQDDLARLMTLEQGKPLAEAKGEISYAASFIEWFA 120
              W+A TAKER+ +LR WF L+M  Q+DLA+LMT EQGKPLAEAKGE++Y ASF+EWFA
Sbjct: 62  WGPWKAKTAKERSAVLRRWFELIMAAQNDLAKLMTAEQGKPLAEAKGEVAYGASFVEWFA 121

Query: 121 EEGKRIYGDTIPGHQADKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLK 180
           EE KR+YGDTIP H   +R++V+K+PIGV AAITPWNFP AMITRK  PALAAGC +V+K
Sbjct: 122 EEAKRVYGDTIPEHMPGRRIVVVKEPIGVVAAITPWNFPLAMITRKCAPALAAGCPVVVK 181

Query: 181 PASQTPFSALALAELAIRAGVPAGVFNVVT-GSAGAVGNELTSNPLVRKLSFTGSTEIGR 239
           PA  TP SALALAELA RAG P GVFNV+T G   AVG ELT+NP VRKLSFTGSTE+G+
Sbjct: 182 PAEDTPLSALALAELAERAGFPPGVFNVITAGDPKAVGFELTANPKVRKLSFTGSTEVGK 241

Query: 240 QLMEQCAKDIKKVSLELGGNAPFIVFDDADLDKAVEGALASKFRNAGQTCVCANRLYVQD 299
            LM QCA  +KK+SLELGGNAPF+VFDDADLD AV GA+ASK+RN GQTCVCANRL VQD
Sbjct: 242 LLMAQCAATVKKLSLELGGNAPFMVFDDADLDAAVAGAMASKYRNTGQTCVCANRLLVQD 301

Query: 300 GVYDRFAEKLQQAVSKLHIGDGLDNGVTIGPLIDEKAVAKVEEHIADALEKGARVVCGGK 359
           G+YD F  +L +AV+ L +G GL+     GPLI+E+AV KVE HIADA+ KGARVV GGK
Sbjct: 302 GIYDAFTARLAEAVAALKVGPGLEGDFQQGPLINEEAVRKVERHIADAVAKGARVVMGGK 361

Query: 360 AHERGGNFFQPTILVDVPANAKVSKEETFGPLAPLFRFKDEADVIAQANDTEFGLAAYFY 419
            H RGG FF+PTIL DV  +   ++EETFGP+APLFRFK E + +  ANDTEFGLAAYFY
Sbjct: 362 RHARGGTFFEPTILADVTPDMAPAREETFGPVAPLFRFKTEEEAVRMANDTEFGLAAYFY 421

Query: 420 ARDLSRVFRVGEALEYGIVGINTGIISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYMC 479
           +RD+ RV+RV  ALEYGIVGIN G+IS EVAPFGG+K SGLGREGSKYGIED+LE+KY+C
Sbjct: 422 SRDVGRVWRVSRALEYGIVGINEGLISTEVAPFGGVKESGLGREGSKYGIEDFLEVKYLC 481

Query: 480 IG 481
           +G
Sbjct: 482 MG 483


Lambda     K      H
   0.318    0.135    0.395 

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: 718
Number of extensions: 18
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: 482
Length of database: 485
Length adjustment: 34
Effective length of query: 448
Effective length of database: 451
Effective search space:   202048
Effective search space used:   202048
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