GapMind for catabolism of small carbon sources

 

Aligments for a candidate for malEIICB in Sphingomonas koreensis DSMZ 15582

Align The Maltose group translocator, MalT of 470 aas and 10 TMSs. Takes up extracellular maltose, releasing maltose-phosphate into the cytoplasm (characterized)
to candidate Ga0059261_1647 Ga0059261_1647 PTS system, N-acetylglucosamine-specific IIBC component

Query= TCDB::Q63GK8
         (545 letters)



>lcl|FitnessBrowser__Korea:Ga0059261_1647 Ga0059261_1647 PTS system,
           N-acetylglucosamine-specific IIBC component
          Length = 560

 Score =  197 bits (500), Expect = 1e-54
 Identities = 172/550 (31%), Positives = 246/550 (44%), Gaps = 93/550 (16%)

Query: 10  QKFGKALLVVVAVMPAAGLMISIGKLIGMSAGDINAVHTIARVMEDIGWAIITNLHILFA 69
           Q  G+AL++ +AV+P AGL++ IG+   +    ++A           G AI  NL ILFA
Sbjct: 9   QPLGRALMLPIAVLPVAGLLLRIGQPDLLDIAFVSAA----------GTAIFGNLGILFA 58

Query: 70  VAIGGSWAKDRAGGAFAALLAFVLTNRITGAIFGVNAEM----LADSKAKVSSVLAGDLI 125
           + +   +A+D  G A  A +   L +      F +        L D+ AKV        +
Sbjct: 59  IGVAVGFARDGNGAAALAGVTCYLVSTTGAQTFLIAPPEVVAGLPDAAAKV--------V 110

Query: 126 VKDYFTSVLGAPALNMGVFVGIITGFLGATLYNKYYNYNKLPQALAFFNGKRFVPFVVIV 185
            + + T  +      + V +GII+G +G   YN++     LP+ LAFF G+RFVP    +
Sbjct: 111 AQAWATGQID----RLEVPIGIISGLIGGKFYNRFATI-ALPEYLAFFGGRRFVPIAAGI 165

Query: 186 WSTVTAIVLSLLWPFIQSGLNEFGRWIAASKDSAPIVAPFVYGTLERLLLPFGLHHMLTI 245
              + A VL   +  I S L+     +  S  +      FVYG L RLLL  GLHH+L  
Sbjct: 166 AGLLLAGVLGYGYAHISSALDAASHAVVESGGA----GMFVYGVLNRLLLVTGLHHLLNN 221

Query: 246 PMNYTELGGTYTMLTGSKVGQVVAGQDPLWLAWITDLNNLLANGDTKAYNDLLNNVVPAR 305
              +  L G +   TG                   DL    A GD  A            
Sbjct: 222 VAWF--LVGDFGGATG-------------------DLGRFFA-GDPNA----------GA 249

Query: 306 FKAGQVIGSTAALMGIAFAMFRNVDKEKRAKYKPMFLSAALAVFLTGVTEPIEFMFMFIA 365
           F +G        L     AM+     E+R     M  S A   FLTGVTEPIEF FMF+A
Sbjct: 250 FMSGFFPVMMFGLPAACLAMYHEARPERRKAVGGMLFSLAFTSFLTGVTEPIEFTFMFLA 309

Query: 366 PVLYVVYAITTGLAFALADLINLRVHAFGFIELITRTPMMVNAGLTRDLINFVI------ 419
           PVLY ++A+ TG+A  L D++ +++  FGF           +AGL   ++NF +      
Sbjct: 310 PVLYAIHAVLTGVAMTLMDMLGIKL-GFGF-----------SAGLFDYVLNFKLSTRPWM 357

Query: 420 ---VSLVFFGLNFTLFNFLIKKFNLPTPGRAGNYIDNEDEASEGTGNVQDGS-LATKVID 475
              V   +  + +TLF F I+K +L TPGR       + EA    G    G+      + 
Sbjct: 358 LLPVGAAYAVIYYTLFRFFIRKLDLATPGR------EKGEAVAAAGETAAGNERGAAFVK 411

Query: 476 LLGGKENIADVDACMTRLRVTVKDLDVVAPEAQWKQNGALGLI-VKDKGVQAVYGPKADV 534
            LGG  N+  VDAC TRLR+ V D   V  +A     GA G+I       Q V GP AD+
Sbjct: 412 ALGGAANLTSVDACTTRLRLIVADQSAV-DDAALNALGARGIIRPSANATQVVLGPIADL 470

Query: 535 LKSDIQDMLG 544
           +  +I+  +G
Sbjct: 471 VAEEIRGAIG 480


Lambda     K      H
   0.325    0.140    0.416 

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: 715
Number of extensions: 35
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 545
Length of database: 560
Length adjustment: 36
Effective length of query: 509
Effective length of database: 524
Effective search space:   266716
Effective search space used:   266716
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: 53 (25.0 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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