Alignments for a candidate for gabD in Marinobacter adhaerens HP15

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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources