GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucDH in Caulobacter crescentus NA1000

Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate CCNA_00092 CCNA_00092 short chain dehydrogenase

Query= uniprot:B2T9V3
         (247 letters)



>FitnessBrowser__Caulo:CCNA_00092
          Length = 296

 Score =  145 bits (365), Expect = 1e-39
 Identities = 105/265 (39%), Positives = 141/265 (53%), Gaps = 32/265 (12%)

Query: 1   MTQRLAGKTALITAAGQGIGLATAELFAREGARVIATDIRIDGLAGKPVEARKLD----- 55
           M  RL GK A+IT    GIGL T ELF  EGA V+A D++ +   G+ +E R  D     
Sbjct: 1   MVGRLNGKVAVITGGCSGIGLGTVELFVAEGACVVAADLQDE--KGRMLEQRFPDQVRFA 58

Query: 56  ----VRDDAAIKALA---AEIGAVDVLFNCAGFVHAG---NILECSEEDWDFAFDLNVKA 105
                 DD   K +A   +  G +D+LFN AG  H G   ++ E + E WD  F L V+ 
Sbjct: 59  RCDVTADDDLAKTMALAESSFGGLDILFNNAG--HGGTPASVPELTAEAWDKTFALLVRG 116

Query: 106 MYRMIRAFLPAMLDKGGGSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFITR 165
               +   LP M  +GGGSIIN +S A    G     AYS++KAAVI +++  AA+   +
Sbjct: 117 PAMGMTHALPLMQKRGGGSIINTASIAGLQAGF-GPLAYSSAKAAVIHMSRCAAAELSPQ 175

Query: 166 GVRCNAICPGTVA------SPSLEQRIVAQAQAQGATLDAVQAAFVARQPMGRIGKPEEI 219
            +R NAICPG +A      S  L + +  Q  AQ A++          QP+ + G PE+I
Sbjct: 176 KIRVNAICPGLIATSIFGASMGLPREVADQMAAQIASIGP------KIQPIPKSGLPEDI 229

Query: 220 AALALYLGSDESSFTTGHAHVIDGG 244
           AA ALYL SD+S F TG   V+DGG
Sbjct: 230 AAAALYLASDDSRFVTGTHIVVDGG 254


Lambda     K      H
   0.320    0.133    0.381 

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: 186
Number of extensions: 6
Number of successful extensions: 4
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: 247
Length of database: 296
Length adjustment: 25
Effective length of query: 222
Effective length of database: 271
Effective search space:    60162
Effective search space used:    60162
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 bits)

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

Links

Downloads

Related tools

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