Alignments for a candidate for gabD in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for gabD in Cupriavidus basilensis 4G11

Align NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized)
to candidate RR42_RS21760 RR42_RS21760 succinate-semialdehyde dehydrogenase

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



>FitnessBrowser__Cup4G11:RR42_RS21760
          Length = 482

 Score =  702 bits (1813), Expect = 0.0
 Identities = 349/480 (72%), Positives = 404/480 (84%), Gaps = 4/480 (0%)

Query: 1   MQLKDAQLFRQQAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKA 60
           +QL+D  L RQQ +IDG W DA   + I V NPATGE +G VP +GA ETR+AIEAA++A
Sbjct: 2   LQLQDPSLLRQQCYIDGRWTDAQ--RHIDVTNPATGERVGQVPLLGADETRQAIEAANRA 59

Query: 61  LPAWRALTAKERATKLRRWYELLIENQDDLGRLMTLEQGKPLAEAKGEIAYAASFIEWFA 120
           LPAWRA TAKER+  LR+W+ELL+ NQDDL R+MT EQGKP AEA+GEI YAASFIEWFA
Sbjct: 60  LPAWRARTAKERSALLRKWFELLLANQDDLARIMTAEQGKPFAEARGEIGYAASFIEWFA 119

Query: 121 EEAKRIYGDVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVIK 180
           EE KR+YG+ IP    ++R++V K+P+GV AAITPWNFPAAMITRKAGPALAAGCTMV+K
Sbjct: 120 EEGKRVYGETIPAPVSNQRIVVTKEPVGVCAAITPWNFPAAMITRKAGPALAAGCTMVVK 179

Query: 181 PASQTPFSALALVELAHRAGIPKGVLSVVTGSAGDIGGELTSNPIVRKLSFTGSTEIGRQ 240
           PASQTP +ALA+V LA RAGIP GVLSVVTGSA  IGGEL+SNP+VRKL+FTGSTE+GR 
Sbjct: 180 PASQTPLTALAMVALAERAGIPAGVLSVVTGSAAAIGGELSSNPLVRKLTFTGSTEVGRT 239

Query: 241 LMAECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDS 300
           LMA+ A  IKKVS+ELGGNAPFIVF+DADLD AVEGAI+SKYRN GQTCVCANRLY+   
Sbjct: 240 LMAQTASTIKKVSMELGGNAPFIVFEDADLDAAVEGAIVSKYRNAGQTCVCANRLYVHSK 299

Query: 301 VYDAFAEKLKAAVAKLKIGNGLEEGTTTGPLIDEKAVAKVQEHIADALKKGATLLAGGK- 359
           VYDAFAEKL AAV  LK+GNG+E+G   GPLID KAV KV+EHI DA+ KGA +L GGK 
Sbjct: 300 VYDAFAEKLVAAVRALKVGNGMEDGVRIGPLIDGKAVTKVEEHITDAISKGARVLQGGKR 359

Query: 360 -SMEGNFFEPTILVNVPKDAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYA 418
            ++  +FFEPT+L +V     VA+EETFGPLAPLFRF+ E EV+AM+NDTEFGLASYFYA
Sbjct: 360 HALGQSFFEPTVLADVTPGMLVAREETFGPLAPLFRFETEDEVVAMANDTEFGLASYFYA 419

Query: 419 RDLGRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCL 478
           RDLGRV+RV+E LEYGMVGVNTGLISNEVAPFGG+K SG+GREGS YGIEDYL IKY C+
Sbjct: 420 RDLGRVWRVSERLEYGMVGVNTGLISNEVAPFGGVKQSGVGREGSHYGIEDYLVIKYTCM 479


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: 705
Number of extensions: 14
Number of successful extensions: 3
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: 482
Length adjustment: 34
Effective length of query: 446
Effective length of database: 448
Effective search space:   199808
Effective search space used:   199808
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: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

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 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