GapMind for catabolism of small carbon sources

 

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

Align Alpha-ketoglutarate permease, MFS superfamily (characterized)
to candidate AO353_26710 AO353_26710 citrate-proton symporter

Query= reanno::pseudo3_N2E3:AO353_03810
         (439 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_26710
          Length = 434

 Score =  241 bits (616), Expect = 2e-68
 Identities = 134/413 (32%), Positives = 215/413 (52%), Gaps = 5/413 (1%)

Query: 23  SRIKSIFSGSVGNMVEWYDWYVYAAFSLYFAKAFFPKGDTTAQLLNTAAIFAVGFLMRPI 82
           S++ +IF  + GN +E +D++++  ++ Y A AFFP     A L+ T A+F  GFLMRP+
Sbjct: 14  SKVSAIFRVTSGNFLEQFDFFLFGFYATYIAAAFFPASSEFASLMMTFAVFGAGFLMRPL 73

Query: 83  GGWLMGLYADRAGRKAALMASVYLMCFGSLIIALSPGYETIGVGAPILLVFARLLQGLSV 142
           G  ++G Y D  GR+  L+ ++ +M  G+++I L PGYETIG+ AP L++  RLLQG S 
Sbjct: 74  GAVILGAYIDDVGRRKGLIVTLSIMASGTILIVLVPGYETIGLFAPALVLIGRLLQGFSA 133

Query: 143 GGEYGTSATYLSEMATKERRGFFSSFQYVTLISGQLIALGVLIVLQQTLTTEQLYDWGWR 202
           G E G  + YL+E+AT  R+GFF+S+Q  +     ++A  +   L Q +    + DWGWR
Sbjct: 134 GAELGGVSVYLAEIATPGRKGFFTSWQSASQQVAIVVAAALGYALNQWMPATVVADWGWR 193

Query: 203 IPFAIGALCAIVALYLRRGMEETESFA--KKEKSKESAMRTLLRHPKELMTVVGLTMGGT 260
           IPF +G +       LRR +EET  F   +   S      TLL++ + ++  + +    T
Sbjct: 194 IPFFVGCMIVPFIFLLRRSLEETAEFTARRHRPSMRQVFGTLLQNWQIVIAGMLMVALTT 253

Query: 261 LAFYTYTTYMQKYLVNTVGMSISDSTTISAATLFLFMCLQPIIGGLSDKVGRRPILIAFG 320
            AFY  T Y   +    + +S SD+  ++        C  P+ G LSD++GRRP+L+A  
Sbjct: 254 TAFYLITVYAPTFGKTVLHLSTSDALLVTLLVGVSNFCWLPLGGALSDRIGRRPVLVAMT 313

Query: 321 ILGTLFTVPILTTLHTIQTWWGAFFLIMAALIIVSGYTSINAVVKAELFPTEIRALGVGL 380
           +L      P LT L    ++     +++    I   Y         E+ P E+R  G  L
Sbjct: 314 LLTLATAYPALTYLVQAPSFINMLLVLLWLSFIYGLYNGAMVAALTEIMPVEVRVAGFSL 373

Query: 381 PYALTVSIFGGTAEYIA---LWFKSIGMETGYYWYVTACIAVSLLVYVTMKDT 430
            Y+L  ++FGG    I+   + +       GY+    A  A+   +Y+  + T
Sbjct: 374 AYSLATAVFGGFTPAISTFLIQYSGDKAAPGYWMSFAALCALCATLYLYRRST 426


Lambda     K      H
   0.325    0.138    0.414 

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: 545
Number of extensions: 34
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: 439
Length of database: 434
Length adjustment: 32
Effective length of query: 407
Effective length of database: 402
Effective search space:   163614
Effective search space used:   163614
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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