GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Herbaspirillum seropedicae SmR1

Align Fructokinase (EC 2.7.1.4) (characterized)
to candidate HSERO_RS02180 HSERO_RS02180 fructokinase

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



>FitnessBrowser__HerbieS:HSERO_RS02180
          Length = 301

 Score =  285 bits (728), Expect = 1e-81
 Identities = 148/300 (49%), Positives = 204/300 (68%), Gaps = 5/300 (1%)

Query: 4   QLPSVVVFGEALTDVVQHSPGRWQGYPGGAPWNVARAMSRLGVPTAFAGSISTDSLGDEL 63
           Q  + VVFGEALTD ++    +W+  PGGA WNVARA +RLGVPT +AGS+STD  G EL
Sbjct: 3   QSAAFVVFGEALTDFIRQPDEQWRAIPGGACWNVARAAARLGVPTGYAGSVSTDVFGAEL 62

Query: 64  AQQSKAAGLDMRFLQRVDADPLVAIVPSSHPPRYFFAGE--ADLLFDVDQLPAGWLDAAR 121
              ++AAGLDMRF Q+    PL+A+V S+ PP YFF G+  ADL FD  +LPAGWLD A+
Sbjct: 63  YALTQAAGLDMRFTQQYAKAPLLAMVTSTTPPDYFFIGDDSADLHFDPQRLPAGWLDDAQ 122

Query: 122 LCHFSCISLARQPLGDRLVEVARRVKEEDKLISYDPNWRNLMDTRYRELTFPAMVELADI 181
           + HF CISL R+PL  RL+++A+     +K I++DPNWR LMD+    L F  ++ L+  
Sbjct: 123 VLHFGCISLTREPLASRLLQIAQEAARRNKKIAFDPNWRKLMDSPSYRLLFQQLLSLSHY 182

Query: 182 IKLSDEDLRQIYPGLNEEQALHTLRTMNASAQILFTRGAKGMALYAADVKFEQPAIAVEV 241
           +K+SDEDL +++PG  +  AL TL+++   A+IL+T GAKGM     +   +QPA  VEV
Sbjct: 183 VKVSDEDLERLFPG--DTNALATLQSLAPQAEILYTLGAKGMQWIKGEQVIDQPAYRVEV 240

Query: 242 ADTVGAGDSSMAGWLASTLLGIQEP-HARLEFSAACASVSCSHAGAYAPSREEVEDLLSN 300
            DTVG GD+SM GW+AS L     P    L+ +AA A+++ S AGAYA + +EV+ L+++
Sbjct: 241 IDTVGCGDASMGGWIASQLRQPDAPAQVHLQCAAAGAAIAASKAGAYAATWDEVQALIAH 300


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: 270
Number of extensions: 5
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: 306
Length of database: 301
Length adjustment: 27
Effective length of query: 279
Effective length of database: 274
Effective search space:    76446
Effective search space used:    76446
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.

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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