GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proP in Brucella microti CCM 4915

Align proline porter II (characterized)
to candidate WP_004687113.1 BMI_RS14180 MFS transporter

Query= CharProtDB::CH_024324
         (500 letters)



>NCBI__GCF_000022745.1:WP_004687113.1
          Length = 632

 Score =  204 bits (518), Expect = 1e-56
 Identities = 116/328 (35%), Positives = 183/328 (55%), Gaps = 16/328 (4%)

Query: 21  GKLRKAITAASLGNAMEWFDFGVYGFVAYALGKVFFPGADPSVQMVAALATFSVPFLIRP 80
           G+ RK I A+SLG   EW+DF +YG +A  +G  FF     + + +  L  F+  FL+RP
Sbjct: 16  GEERKVIFASSLGTVFEWYDFYLYGTLASFIGAAFFNEYPEATRNIFVLLAFAAGFLVRP 75

Query: 81  LGGLFFGMLGDKYGRQKILAITIVIMSISTFCIGLIPSYDTIGIWAPILLLICKMAQGFS 140
            G L FG +GD  GR+    +TIVIM  STF +GL+P   ++GI+API+L+  +M QG +
Sbjct: 76  FGALVFGRIGDLVGRKYTFLVTIVIMGGSTFLVGLLPGSASLGIFAPIILIALRMLQGLA 135

Query: 141 VGGEYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTIVGEANFLDWGW 200
           +GGEY GA+ +VAE++P+ +RGF  SW+   +  G  L   V++   T++ +  F  WGW
Sbjct: 136 LGGEYGGAATYVAEHAPNNRRGFFTSWIQTTATLGLFLSLLVILGAQTLLSKDAFAAWGW 195

Query: 201 RIPFFIALPLGIIGLYLRHALEETPAFQQHVDKLEQGDREGLQDGPKVSFKEIATKYWR- 259
           RIPF +++ L  I +++R  + E+PAF++     E+G         K    E A   W+ 
Sbjct: 196 RIPFLVSVLLLGISVWIRMQMSESPAFKR---MKEEGKTS------KAPLSE-AFGQWKN 245

Query: 260 ---SLLTCIGLVIATNVTYYMLLTYMPSYLSHNLHY-SEDHGVLIIIAIMIGMLFVQPVM 315
              +L+   GL     V +Y    Y   +L + L   ++   +++ IA++IG  F   + 
Sbjct: 246 AKIALIALFGLTAGQAVVWYCGQFYALFFLQNVLKVENQSANIMVAIALLIGTGFF-VIF 304

Query: 316 GLLSDRFGRRPFVLLGSVALFVLAIPAF 343
           G LSD+ GR+P ++ G +   V   P F
Sbjct: 305 GWLSDKIGRKPIIMAGLILAAVTYFPLF 332



 Score = 37.7 bits (86), Expect = 1e-06
 Identities = 26/91 (28%), Positives = 47/91 (51%), Gaps = 2/91 (2%)

Query: 353 LIFAGLLMLAVILNCFTGVMASTLPAMFPTHIRYSALAAAFNI-SVLVAGLTPTLAAWLV 411
           L  A L +L + +    G +A+ L  MFPT IRY+ ++  ++I +    GL P     L 
Sbjct: 533 LTIAILTILVIYVTMVYGPIAAILVEMFPTRIRYTGMSLPYHIGNGWFGGLLPAGVFALS 592

Query: 412 ESSQNLMMPAYYLMVVAVVGLITGVT-MKET 441
            +  ++    +Y +++A V  + G+  +KET
Sbjct: 593 AAKGDIYYGLWYPIIIASVTFVIGMLFVKET 623


Lambda     K      H
   0.327    0.142    0.429 

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: 758
Number of extensions: 38
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 500
Length of database: 632
Length adjustment: 36
Effective length of query: 464
Effective length of database: 596
Effective search space:   276544
Effective search space used:   276544
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: 53 (25.0 bits)

This GapMind analysis is from Sep 24 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