GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Cupriavidus basilensis 4G11

Align Fructokinase (EC 2.7.1.4) (characterized)
to candidate RR42_RS03385 RR42_RS03385 sugar kinase

Query= reanno::pseudo6_N2E2:Pf6N2E2_1965
         (306 letters)



>FitnessBrowser__Cup4G11:RR42_RS03385
          Length = 309

 Score =  293 bits (749), Expect = 5e-84
 Identities = 156/296 (52%), Positives = 197/296 (66%), Gaps = 3/296 (1%)

Query: 6   PSVVVFGEALTDVVQHSPGRWQGYPGGAPWNVARAMSRLGVPTAFAGSISTDSLGDELAQ 65
           P+ VVFGEALTD+V      W G PGG+ WNVAR  +RLGVPTAFAG+IS D+LGD+LA+
Sbjct: 7   PAYVVFGEALTDMVHQGGQDWLGLPGGSCWNVARVGARLGVPTAFAGAISADTLGDQLAE 66

Query: 66  QSKAAGLDMRFLQRVDADPLVAIVPSSHPPRYFFAGE--ADLLFDVDQLPAGWLDAARLC 123
            S  AGLD+RFLQRV+  PL+A V + HPP+YFF G+  ADL FD ++LP GW  AAR  
Sbjct: 67  ASAEAGLDLRFLQRVERSPLLAFVGAQHPPQYFFVGDDSADLYFDPERLPPGWRQAARTV 126

Query: 124 HFSCISLARQPLGDRLVEVARRVKEEDKLISYDPNWRNLMDTRYRELTFPAMVELADIIK 183
           HF  +SLARQPL  RL   A + +   K I++DPN+R  M     +  F  M  LAD IK
Sbjct: 127 HFGSLSLARQPLAARLCTEATQARAAGKRIAFDPNFRTPMRAPEYQAVFAHMAGLADYIK 186

Query: 184 LSDEDLRQIYPGLNEEQALHTLRTMNASAQILFTRGAKGMALYAADVKFEQPAIAVEVAD 243
           +SDEDLR +YP L+E  AL  LR +   A++L TRGA GM L   D   EQP  AV+V D
Sbjct: 187 VSDEDLRGLYPALDEHAALAALRALAPQARVLLTRGADGMTLLHGDGACEQPVFAVDVVD 246

Query: 244 TVGAGDSSMAGWLASTLLGIQEPHAR-LEFSAACASVSCSHAGAYAPSREEVEDLL 298
           TVG GD++M GW+A  LL  +   AR   ++AA A+V+ + AGAY+P+  EV  LL
Sbjct: 247 TVGCGDAAMGGWMAGLLLDPEATLARQARWAAATAAVAATRAGAYSPTVAEVSVLL 302


Lambda     K      H
   0.320    0.133    0.398 

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: 288
Number of extensions: 7
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: 306
Length of database: 309
Length adjustment: 27
Effective length of query: 279
Effective length of database: 282
Effective search space:    78678
Effective search space used:    78678
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: 48 (23.1 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