GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Marinobacter adhaerens HP15

Align succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized)
to candidate GFF2064 HP15_2020 succinate-semialdehyde dehydrogenase I

Query= BRENDA::P25526
         (482 letters)



>FitnessBrowser__Marino:GFF2064
          Length = 489

 Score =  637 bits (1643), Expect = 0.0
 Identities = 305/484 (63%), Positives = 383/484 (79%), Gaps = 3/484 (0%)

Query: 1   MKLNDSNLFRQQALINGEWLDANNGEAIDVTNPANGDKLGSVPKMGADETRAAIDAANRA 60
           ++L +  L R+QA ING+W+ A +G+   V +PANG++L +VP M   + RAAI+AA+ A
Sbjct: 3   LELKNRELLREQAYINGQWITAKSGKTFAVNDPANGEQLATVPDMDDTDARAAIEAASAA 62

Query: 61  LPAWRALTAKERATILRNWFNLMMEHQDDLARLMTLEQGKPLAEAKGEISYAASFIEWFA 120
            PAWR+  AKERA ILR WFNL+M +Q+DLARLMT EQGKPLAE++GE+ Y ASFIEWFA
Sbjct: 63  WPAWRSTPAKERANILRKWFNLLMANQEDLARLMTAEQGKPLAESRGEVGYGASFIEWFA 122

Query: 121 EEGKRIYGDTIPGHQADKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLK 180
           EE KR YGD IPGH  DKR++VIKQP+GV AAITPWNFP AMITRK  PALAAGC +V+K
Sbjct: 123 EEAKRAYGDVIPGHGKDKRIVVIKQPVGVVAAITPWNFPIAMITRKVAPALAAGCPVVVK 182

Query: 181 PASQTPFSALALAELAIRAGVPAGVFNVVTGS---AGAVGNELTSNPLVRKLSFTGSTEI 237
           PA  TP SALA+  LA  AGVPAG+ N++T S   A +VG+ELT NP+VRK+SFTGST +
Sbjct: 183 PAEDTPLSALAITALAEEAGVPAGLINIITCSKPNAVSVGSELTGNPIVRKVSFTGSTPV 242

Query: 238 GRQLMEQCAKDIKKVSLELGGNAPFIVFDDADLDKAVEGALASKFRNAGQTCVCANRLYV 297
           G+ LM Q +  +KKVSLELGGNAPFIVFDDADLD AV G +ASK+RN GQTCVCANR+YV
Sbjct: 243 GKLLMRQASDTVKKVSLELGGNAPFIVFDDADLDAAVAGLMASKYRNTGQTCVCANRVYV 302

Query: 298 QDGVYDRFAEKLQQAVSKLHIGDGLDNGVTIGPLIDEKAVAKVEEHIADALEKGARVVCG 357
           Q GVYD FAEKL+ AVSK+ +G GL+     GPLI++ A+AKV+ HI DA  KGA+V  G
Sbjct: 303 QAGVYDAFAEKLKAAVSKMVVGPGLEGETQQGPLINDAALAKVKRHIEDATSKGAKVALG 362

Query: 358 GKAHERGGNFFQPTILVDVPANAKVSKEETFGPLAPLFRFKDEADVIAQANDTEFGLAAY 417
           G+AH  GG FF+PTIL        +++EETFGP+APLF+F+ + + IA AND+EFGL+AY
Sbjct: 363 GRAHSLGGTFFEPTILTHATQEMLIAREETFGPVAPLFKFETDDEAIAMANDSEFGLSAY 422

Query: 418 FYARDLSRVFRVGEALEYGIVGINTGIISNEVAPFGGIKASGLGREGSKYGIEDYLEIKY 477
           FY+R++ RV+RV E LE G++G+N GIIS EVAPFGG+K SGLGREGS YG+++Y+E+KY
Sbjct: 423 FYSRNIHRVWRVAEELESGMIGVNEGIISTEVAPFGGVKESGLGREGSHYGLDEYMELKY 482

Query: 478 MCIG 481
           +C+G
Sbjct: 483 LCLG 486


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: 743
Number of extensions: 19
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: 489
Length adjustment: 34
Effective length of query: 448
Effective length of database: 455
Effective search space:   203840
Effective search space used:   203840
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