GapMind for catabolism of small carbon sources

 

Aligments for a candidate for malEIICB in Shewanella loihica PV-4

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 5210198 Shew_2641 PTS system, glucose-like IIB subunint (RefSeq)

Query= TCDB::Q63GK8
         (545 letters)



>lcl|FitnessBrowser__PV4:5210198 Shew_2641 PTS system, glucose-like
           IIB subunint (RefSeq)
          Length = 490

 Score =  207 bits (528), Expect = 6e-58
 Identities = 164/539 (30%), Positives = 272/539 (50%), Gaps = 78/539 (14%)

Query: 6   FDFWQKFGKALLVVVAVMPAAGLMISIGKLIGMSAGDINAVHT-IARVMEDIGWAIITNL 64
           F F Q+  +ALL+ +A++PAAG+MI      G++   I  +   +A +M  +G  + + +
Sbjct: 24  FKFAQRLSQALLLPIAILPAAGVMI------GLATNPIPFISADLATLMWTVGNLVFSMM 77

Query: 65  HILFAVAIGGSWAKDRAGGAFAALLAFVLTNRITGAIFGVNAEMLADSKAKVSSVLAGDL 124
            +LFAV I   + +D+   AF+A+  +       G  F              SS+ A   
Sbjct: 78  PMLFAVTIAIGFCRDQGIAAFSAVFGY-------GVFF--------------SSLSALAK 116

Query: 125 IVKDYFTSVLGAPALNMGVFVGIITGFLGATLYNKYYNYNKLPQALAFFNGKRFVPFVVI 184
           I       +LG   ++ G+  G++ G     L  K+    +LP   +FF G+R  P +++
Sbjct: 117 IYHLPTEMILGQATIDTGIAGGMMVGAF-TCLVVKHSERIRLPAVFSFFEGRRSAPLLML 175

Query: 185 VWSTVTAIVLSLLWPFIQSGLNEFGRWIAASKDSAPIVAPFVYGTLERLLLPFGLHHMLT 244
             + + A +  LLWP + + + +   W    +   P  A  VYG +ERLL+P GLHH+  
Sbjct: 176 PMAILLAYLFLLLWPLLSNWIEQISNWAVYQE---PASAFAVYGMVERLLIPLGLHHIWN 232

Query: 245 IPMNYTELGGTYTMLTGSKVGQVVAGQDPLWLAWITDLNNLLANGDTKAYNDLLNNVVPA 304
            P  Y E+G  +         + V G+   +LA           GD +A N         
Sbjct: 233 APF-YLEMGQYFNG------DEWVRGEVARYLA-----------GDPQAGN--------- 265

Query: 305 RFKAGQVIGSTAALMGIAFAMFRNVDKEKRAKYKPMFLSAALAVFLTGVTEPIEFMFMFI 364
              AG  +     L   A A++R  DK +R +   + LSAA A +LTGVTEPIEF FMF+
Sbjct: 266 --LAGGYLIKMWGLPAAALAIWRCADKHERNRVAGIMLSAATACWLTGVTEPIEFAFMFV 323

Query: 365 APVLYVVYAITTGLAFALADLINLRVHAFGFIELITRTPMMVNAGLTRDLINFVIVSLVF 424
           AP+L++++A+ TG+A+A+   +++  H+  F   +    +++  G +R++  F+I+  + 
Sbjct: 324 APLLFILHALMTGIAYAVTISLDIH-HSVVFSHGLVDFSLLL--GQSRNVEWFLILGPLT 380

Query: 425 FGLNFTLFNFLIKKFNLPTPGRAGNYIDNEDEASEGTGNVQDGSLATKVIDLLGGKENIA 484
             + + +F   I  FNL TPGR         EA  G    Q   L + +I  LGG++NI 
Sbjct: 381 AVIYYLVFRGAILAFNLKTPGRM--------EAGSG----QRAGLIS-MITALGGQDNIN 427

Query: 485 DVDACMTRLRVTVKDLDVVAPEAQWKQNGALGLIVKDKGVQAVYGPKADVLKSDIQDML 543
           ++ AC+TRLR++VK  ++V  +AQ  + GA G+++   GVQ VYG KA+ ++  +Q  L
Sbjct: 428 ELTACLTRLRISVKHAELV-DKAQLNKLGAKGVVLVGNGVQLVYGTKAESIRRLLQRYL 485


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: 626
Number of extensions: 31
Number of successful extensions: 6
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: 545
Length of database: 490
Length adjustment: 35
Effective length of query: 510
Effective length of database: 455
Effective search space:   232050
Effective search space used:   232050
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: 52 (24.6 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 paper from 2022 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