GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruK in Acidovorax sp. GW101-3H11

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate Ac3H11_609 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)

Query= SwissProt::Q8G847
         (513 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_609
          Length = 505

 Score =  314 bits (805), Expect = 4e-90
 Identities = 178/513 (34%), Positives = 306/513 (59%), Gaps = 22/513 (4%)

Query: 7   IVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINA--GSI 64
           ++ M+ I   FPGV AL+ V+L +  GE+HA++GENGAGKST++K L+GVY   +  G I
Sbjct: 2   LLEMRNIRKTFPGVVALNQVNLQVQAGEIHAIVGENGAGKSTLMKVLSGVYPHGSYSGQI 61

Query: 65  MVDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEAA 124
           + DG+ ++F G  D+++ GI  ++QE+ L   LS+ EN+ LG+E      IDW   H  A
Sbjct: 62  LFDGQEREFAGIRDSEHLGIIIIHQELALVPLLSIAENIFLGNETARHGVIDWMAAHSRA 121

Query: 125 KKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLF 184
           +  L ++GL    P TP+  + +  QQLV IA+A+    ++LILDEPT+SL+ N+ + L 
Sbjct: 122 QALLHKVGLGE-SPDTPVGQLGVGKQQLVEIAKALSRKVRLLILDEPTASLNENDSQALL 180

Query: 185 AIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTP--RDELIGMMIG 242
            ++ +++  G+  + +SH L++I  + D +T+LR+G  ++ +  ++ P   D +I  M+G
Sbjct: 181 DLLLELKAQGITCILISHKLNEISRVADAITVLRDGSTVQMLDCREGPVSEDRVIQAMVG 240

Query: 243 KSAAELSQIGAKKARREITPGEKPIVDVKGL-------GKKGTINPVDVDIYKGEVVGFA 295
           +  ++      +  +R+   GE  + +V+           +  +  +D+++ +GE+VG A
Sbjct: 241 REMSD------RYPQRQPQVGEI-VFEVRNWRAHHPQRSDREHLKGIDLNVRRGEIVGIA 293

Query: 296 GLLGSGRTELGRLLYGAD--KPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGII 353
           GL+G+GRTEL   ++G    +  SG   L+G+ +++S    A+ + +AY TE+R+  G++
Sbjct: 294 GLMGAGRTELAMSIFGRSWGQRISGEVRLHGQPIDVSTVEKAVSHGLAYVTEDRKGNGLV 353

Query: 354 GDLTVRQNILIALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQK 413
            +  ++ N  +A          I   +   +   Y ++L +R +  D+   NLSGGNQQK
Sbjct: 354 LNEDIQFNTSLANLPGVSFASVIDSGQEHRVAQDYREKLRIRCSGVDQKTLNLSGGNQQK 413

Query: 414 VLIGRWLATHPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSD 473
           V++ +WL T PE+LILDEPTRGID+GAK EI  ++  LA++G  V+ ISSE+ E++ ++D
Sbjct: 414 VVLSKWLFTSPEVLILDEPTRGIDVGAKYEIYTLIAQLAAEGKCVIVISSEMPELLGITD 473

Query: 474 DIEVLKDRHKIAEIENDDTVSQATIVETIANTN 506
            I V+ +   +AE+   +  SQ  I+  I   +
Sbjct: 474 RIYVMNEGRFVAEMPTSE-ASQEKIMRAIVKAS 505


Lambda     K      H
   0.316    0.135    0.376 

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: 635
Number of extensions: 36
Number of successful extensions: 9
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: 513
Length of database: 505
Length adjustment: 34
Effective length of query: 479
Effective length of database: 471
Effective search space:   225609
Effective search space used:   225609
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 (21.6 bits)
S2: 52 (24.6 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