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

GapMind for catabolism of small carbon sources

Aligments 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)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_609 L-arabinose
           transport ATP-binding protein AraG (TC 3.A.1.2.2)
          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:

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, or view the source code.

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