GapMind for catabolism of small carbon sources

 

Aligments for a candidate for manMFS in Klebsiella michiganensis M5al

Align D-mannose and D-mannitol transporter (characterized)
to candidate BWI76_RS03930 BWI76_RS03930 MFS transporter

Query= reanno::pseudo5_N2C3_1:AO356_28540
         (430 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS03930 BWI76_RS03930 MFS
           transporter
          Length = 453

 Score =  221 bits (564), Expect = 3e-62
 Identities = 135/411 (32%), Positives = 209/411 (50%), Gaps = 17/411 (4%)

Query: 10  IIMLFLAGVINYLDRSALSVAAPFIQKDYGLSTGEMGMIFSSFFVGYAAFNFIGGWAADR 69
           +I+LFLA VINYLDRS+LSVA   I+++ GLS  E+G + S F + Y       G   DR
Sbjct: 44  MILLFLAAVINYLDRSSLSVANLTIREELGLSATEIGALLSVFSLAYGIAQLPCGPLLDR 103

Query: 70  YGAKTTLLLAMVLWSLFSGLTVLTVGFASLVLIRILFGMGEGPLSVTTSKMVNNWYTPKR 129
            G +  L L M  WSLF  ++ +   F   VL+RI  G+GE P++    K++N+W+  K 
Sbjct: 104 KGPRIMLGLGMFFWSLFQAVSGMVHSFTQFVLVRIGMGIGEAPMNPCGVKVINDWFNIKE 163

Query: 130 RARAIGASMSGTPLGGAISGPVVGFIAVTYGWKISFIIIMLIGLVWAAVWFKFVKERPEG 189
           R R +G   + + +G AIS P++  + +  GW+  FI I L+G+  A  W+   + R   
Sbjct: 164 RGRPMGFFNAASTIGVAISPPILAAMMLMMGWRGMFITIGLLGIFVAIGWYMLYRNR--- 220

Query: 190 EGAEDI-LRAEGQGELAAQPV----FPLRF-----YLKQPTVLFTSLAFFSYNYTLFFFL 239
              EDI L A+ Q  L A  V     PL F       K  T+    L F   NYT + +L
Sbjct: 221 ---EDIALTADEQAYLNAGSVNVRRDPLSFAEWRSLFKNKTMWGMMLGFSGINYTAWLYL 277

Query: 240 TWFPSYLTMAHGLNVKDMSIATVIPWVLGFLGLALGGFISDFVFKKTGRMMFSRKVVLVT 299
            W P YL  A+ L++K       IP++ G  G+ + G+++D++ K     + SRK+ ++ 
Sbjct: 278 AWLPGYLQTAYNLDLKSTGFMAAIPFLFGAAGMLINGYVTDWLVKGGMAPIKSRKICIIA 337

Query: 300 CLLACAVCIACAGMVTTLYPAVILVALAVFFLYLTGAIYWAIIQDTVPAARVGGVSGFMH 359
            +   A         TT   AV+L+ +A+F ++  G   W +I   V +     V    +
Sbjct: 338 GMFCSAAFTLVVPQATTSIVAVLLIGMALFCIHFAGTSCWGLIHVAVASRMTASVGSIQN 397

Query: 360 FLANTSGIVGPTLTGFLVQFTGSFTSAFLLAGLLTVIGAVCVARYVK-PLS 409
           F +       P +TGF+V  T SF  A ++ G +T +GA+     V+ P+S
Sbjct: 398 FASFICASFAPVVTGFIVDTTHSFQLALIICGCVTALGALAYIFLVRQPIS 448


Lambda     K      H
   0.329    0.142    0.439 

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: 496
Number of extensions: 24
Number of successful extensions: 3
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: 430
Length of database: 453
Length adjustment: 32
Effective length of query: 398
Effective length of database: 421
Effective search space:   167558
Effective search space used:   167558
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 (21.8 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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