GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deh in Pseudomonas fluorescens FW300-N2E3

Align Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized)
to candidate AO353_17220 AO353_17220 alpha-ketoglutarate permease

Query= TCDB::M1Q159
         (468 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_17220
          Length = 431

 Score =  223 bits (567), Expect = 1e-62
 Identities = 135/432 (31%), Positives = 230/432 (53%), Gaps = 23/432 (5%)

Query: 11  KGIWKVIFASSAGTVIEWYDFYIFGALATTLASKFYNTGTPIGDIIAWLGTFAVGFLVRP 70
           K I+ ++ ASS G ++EW+DFY++   A   A  F+ +  P   ++   G FA GFL+RP
Sbjct: 15  KRIFAIVGASS-GNLVEWFDFYVYAFCAIYFAPAFFPSDNPTVQLVNTAGVFAAGFLMRP 73

Query: 71  FGAIVFGRIGDLVGRKFTYLITITIMGSCTFLIGLLPTQDVLGAWAGIILITMRILQGLA 130
            G  +FGR+ D  GRK + +I++ +M + + LI  LPT   +G WA ++L+  R++QG++
Sbjct: 74  IGGWLFGRVADKHGRKNSMMISVLMMCAGSLLIACLPTYKDIGVWAPLLLLVARLIQGVS 133

Query: 131 LGGQYGGAATFVAEHAPQGKRGFYTSWIQTTATFGLLISLGVILITRISLGEADFNEWGW 190
           +GG+YG  AT+++E A +G+RGF+ S+   T   G L+++ +++I +  L E D   WGW
Sbjct: 134 VGGEYGTTATYMSEVALKGQRGFFASFQYVTLIGGQLLAVSLVVILQQFLTEDDLRAWGW 193

Query: 191 RLPFMASILLVILSLWIRRALKESPLFQQLKDTKAVSKNPLKESFANPYNLRWVLIALFG 250
           R+PF+      ++SL++RR+LKE+   +  ++  A S   L        N     I + G
Sbjct: 194 RIPFVVGAAAALISLFLRRSLKETTSKEMRENKDAGSMAALFR------NNTAAFITVLG 247

Query: 251 ATMGQGVVWYTGQFYALFYLQKIFNTPLIDSNLIVGAALLLSMPFFVFFGSLSDRIGRKK 310
            T G  +++YT   Y   YL      P   ++ I+  AL L M     FG+L+D+IGR+ 
Sbjct: 248 FTAGGSLIFYTFTTYMQKYLVNTAGMPAKTASYIMTGALFLYMCMQPLFGTLADKIGRRN 307

Query: 311 VMLSGMLLAVLTYYPIYGLMAAFAPTDPGQHFLFAYIGYNPVILGLLVFIQVIYVTMVYG 370
            ML    L  L   PI  L+   + T+P       ++ +  + + L +   V + T + G
Sbjct: 308 SMLWFGALGTLFTVPI--LLTLKSVTNP-------FLAFGLITVALAI---VSFYTSISG 355

Query: 371 PIAAFLVELFPTKIRYTSMSLPYHIGNGVFGGLVPMIGLILINATGNDFAGLWWPMAIAG 430
            + A   E+FP ++R   + L Y + N +FGG    + L L  + G + +  W+  A+  
Sbjct: 356 LVKA---EMFPPQVRALGVGLAYAVANAIFGGSAEYVALSL-KSVGIENSFYWYVTAMMA 411

Query: 431 ICLVVGFLLIKE 442
           I  +    L ++
Sbjct: 412 IAFLFSLRLPRQ 423


Lambda     K      H
   0.328    0.144    0.450 

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: 610
Number of extensions: 28
Number of successful extensions: 5
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: 468
Length of database: 431
Length adjustment: 33
Effective length of query: 435
Effective length of database: 398
Effective search space:   173130
Effective search space used:   173130
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (24.3 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