GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruII-ABC in Lactobacillus shenzhenensis LY-73

Align The fructose-specific PTS Enzyme IIABC FruA (characterized)
to candidate WP_040535931.1 L248_RS09200 PTS transporter subunit EIIC

Query= TCDB::Q0S1N2
         (700 letters)



>NCBI__GCF_000469325.1:WP_040535931.1
          Length = 475

 Score =  299 bits (766), Expect = 2e-85
 Identities = 192/484 (39%), Positives = 262/484 (54%), Gaps = 39/484 (8%)

Query: 209 VAVTACPTGIAHTYMAADSLVAAGERAGVVVHVETQGSSG-STPLAPGVIAGASAVIFAT 267
           V VT CP G+AHTYMAA+ L   G+  G  V +ETQG+SG    L P  +  A  VI A 
Sbjct: 5   VGVTKCPVGVAHTYMAAEKLQKVGQSLGYTVKIETQGASGVEDHLTPDDVKNADFVIIAA 64

Query: 268 DVGVKGKERFAGKPVVASGVKRAINEPDTMITEALRAGMNPSAAIVDAGSAGSAADEPA- 326
           DV + G +RF  K V+ S    AI +   +I +A +A +         G    AADE   
Sbjct: 65  DVEIDGMDRFTDKKVLFSTTAAAIKDSAALIDKAKKADIY--------GGKEDAADEKVE 116

Query: 327 GSIGWGTHLRQVLLTGVSYMIPFVAAGGLLIALGFLLGGYEISGPAEDIVLSNSLGQLPE 386
           G     + L + L+ GVS+MIPFV  GGL IAL   LGG+     A  +V  +++     
Sbjct: 117 GDAHEQSPLIKQLMNGVSHMIPFVVVGGLFIALSITLGGHATK--AGMVVAPHTIW---- 170

Query: 387 GGLATYLGAVLFQLGSLAFSFLVPALAGYIAFAIADRPGLAPGFTAGAVA-------VFV 439
                   A + Q+G+L F+ ++P LAGYIA AIA R  LAP   +  VA          
Sbjct: 171 --------ATMNQVGTLGFTLMIPILAGYIATAIAGRAALAPAMLSAMVANSPDILGTKA 222

Query: 440 GAGFIGGLVGGLIAGVVALWISRIPVPQWLRGLMPVVIIPLFATLIVGALMFLVLGRPLA 499
           G GFIG ++ G  AG +  W +  PVP+ LR +MP+ +IPL  T I+       LG P++
Sbjct: 223 GTGFIGAIIVGFAAGYLVKWFNSWPVPKSLRAIMPIFVIPLLGTAIISGAFVFFLGGPIS 282

Query: 500 SITSGLTNWLNGLSGS--SVIFLGIILGLMMCFDLGGPVNKAAYAFAVAGLNVNDPASLR 557
            + + LTN LN LS +  + I LG++LG M+  D+GGP+NK A+ F VA +   +P    
Sbjct: 283 WLMTALTNMLNVLSKNPQTSIILGLLLGAMVSIDMGGPINKVAFLFGVASITAGNP---E 339

Query: 558 IMAAVMAAGMVPPLAMALASTVLRPSLFSEAERENGKAAWLLGSAFISEGAIPFAAADPL 617
           IM AV  A  VPPL+  +A T++R  L S  E   G  A L+G   I+EGAIP A A+P 
Sbjct: 340 IMGAVACAIAVPPLSAGIA-TLIRSDLNSSEETAAGVPAILMGLIGITEGAIPLATANPK 398

Query: 618 RVIPSMMAGGAVTGALIMAFDVTLSAPHGG--IFVFFAIGNLLWFLVALAAGVVVAALCV 675
            V P ++ G AV  A+ M F +T + PHGG  + V  A  NLL F +A+  GV V+A  +
Sbjct: 399 HVFPGIITGSAVAAAIGMFFKITDAVPHGGPIVGVLGATNNLLLFFLAIIIGVAVSAAII 458

Query: 676 VGAK 679
           V  K
Sbjct: 459 VTLK 462


Lambda     K      H
   0.320    0.136    0.395 

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: 785
Number of extensions: 49
Number of successful extensions: 8
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: 700
Length of database: 475
Length adjustment: 36
Effective length of query: 664
Effective length of database: 439
Effective search space:   291496
Effective search space used:   291496
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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