GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kgtP in Pseudomonas fluorescens FW300-N2E2

Align Alpha-ketoglutarate permease, MFS superfamily (characterized)
to candidate Pf6N2E2_1184 L-Proline/Glycine betaine transporter ProP

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



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1184
          Length = 434

 Score =  229 bits (583), Expect = 2e-64
 Identities = 145/416 (34%), Positives = 217/416 (52%), Gaps = 10/416 (2%)

Query: 24  RIKSIFSGSVGNMVEWYDWYVYAAFSLYFAKAFFPKGDTTAQLLNTAAIFAVGFLMRPIG 83
           R K + + SVG  +EW+D+ ++A FSL  A AFFP  D    LL +    AVGF+ RP+G
Sbjct: 8   RRKLVLAVSVGAALEWFDFTLFAIFSLQIAAAFFPASDPLMSLLASYLALAVGFVARPLG 67

Query: 84  GWLMGLYADRAGRKAALMASVYLMCFGSLIIALSPGYETIGVGAPILLVFARLLQGLSVG 143
             LMG YADR GRKAAL  S+ LM  G+LIIA+ P YETIG  AP+ +V AR+LQG++ G
Sbjct: 68  ALLMGRYADRQGRKAALTLSIMLMGAGTLIIAVCPTYETIGWWAPLSVVVARILQGVAAG 127

Query: 144 GEYGTSATYLSEMATKERRGFFSSFQYVTLISGQLIALGVLIVLQQTLTTEQLYDWGWRI 203
           GE G +  YL E A  +RR  F+S Q V      L+      +L   LT  QL +WGWR+
Sbjct: 128 GEIGGALAYLVETAPADRRALFASSQQVAQAGSFLLCGLSASLLSSALTPAQLDEWGWRV 187

Query: 204 PFAIGALCAIVALYLRRGMEETESFAK-KEKSKESAMRTLLRHPKELMTVVGLTMGGTL- 261
           P+  G L  +  L +RR +EE+E   +  +   + AM    + P     +  L MG  + 
Sbjct: 188 PYVFGLLVVVAGLKIRRSLEESEPLRRFLDNQDKHAMAG--KGPSLRPYLPNLVMGVLIV 245

Query: 262 AFYTYTTYMQKYLVNTVGMSIS---DSTTISAATLFLFMCLQPIIGGLSDKVGRRPILIA 318
             +T  T +  ++     M +    +   +    + L   L P+   LSD++GR  +++ 
Sbjct: 246 VLWTVATQLINFIPTYASMVLELPRNKAYLGLVLVGLITLLCPLTALLSDRIGRYTVMLI 305

Query: 319 FGILGTLFTVPILTTLHTIQTWWGAFFLIMAALIIVSGYTSINAVVKAELFPTEIRALGV 378
             +   L   P    L+   +         A  +++  YT   A   AELFP ++RALGV
Sbjct: 306 GAVGVALCAYPGFVWLNNSPSLQTLIIFQCALAVLMVLYTGPAAAALAELFPVQVRALGV 365

Query: 379 GLPYALTVSIFG-GTAEYIALWFKSIG--METGYYWYVTACIAVSLLVYVTMKDTR 431
            L YAL+V++FG  T   I L ++  G  +   ++ +  AC++   L +V++   R
Sbjct: 366 SLAYALSVTLFGSATPALITLIYRQSGDALAAAHWLFAAACLSAIPLAWVSLSKYR 421


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: 490
Number of extensions: 25
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