GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malEIICB in Shewanella oneidensis MR-1

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 200788 SO1623 PTS system, glucose-specific IIBC component (NCBI ptt file)

Query= TCDB::Q63GK8
         (545 letters)



>FitnessBrowser__MR1:200788
          Length = 499

 Score =  207 bits (526), Expect = 1e-57
 Identities = 167/540 (30%), Positives = 270/540 (50%), Gaps = 77/540 (14%)

Query: 6   FDFWQKFGKALLVVVAVMPAAGLMISIGKLIGMSAGDINAVHTIARV-MEDIGWAIITNL 64
           F F Q+  +ALL+ +A++PAAG+M+      G++   I  +  +  V M  +G  I   +
Sbjct: 25  FKFAQRLSQALLIPIAILPAAGVML------GLTVSPIPFMPEVLNVLMLAVGKLIFAIM 78

Query: 65  HILFAVAIGGSWAKDRAGGAFAALLAFVLTNRITGAIFGVNAEMLADSKAKVSSVLAGDL 124
            ILFAVA+   + +D+   AF A+  + +      A        LAD     + +     
Sbjct: 79  PILFAVAVAIGFCRDQGIAAFTAVFGYGVMTATLAA--------LADLYQLPTQL----- 125

Query: 125 IVKDYFTSVLGAPALNMGVFVGIITGFLGATLYN-KYYNYNKLPQALAFFNGKRFVPFVV 183
                   VLG   L+ G+  G++ G  G T +  ++  Y +LP   +FF G+R    ++
Sbjct: 126 --------VLGMETLDTGIAGGMLIG--GVTCFAVRWSQYIRLPAIFSFFEGRRSASLLI 175

Query: 184 IVWSTVTAIVLSLLWPFIQSGLNEFGRWIAASKDSAPIVAPFVYGTLERLLLPFGLHHML 243
           I  +     VL+ +WP +   +     W    K   P +A  VYG LERLL+P GLHH+ 
Sbjct: 176 IPLAMGLGYVLAHIWPSLSLLIERVSDWAVYQK---PAIAFGVYGALERLLIPLGLHHIW 232

Query: 244 TIPMNYTELGGTYTMLTGSKVGQVVAGQDPLWLAWITDLNNLLANGDTKAYNDLLNNVVP 303
             P  Y E+G  Y +    +  +VV G+   +LA           GD +A N        
Sbjct: 233 NAPF-YLEVG-QYQL----QDAEVVRGEVARYLA-----------GDPQAGN-------- 267

Query: 304 ARFKAGQVIGSTAALMGIAFAMFRNVDKEKRAKYKPMFLSAALAVFLTGVTEPIEFMFMF 363
               AG  +     L   A A++R  D  +R +   + LSAA A +LTGVTEPIEF FMF
Sbjct: 268 ---LAGGYLIKMWGLPAAALAIWRCADNSERNRVAGIMLSAAAASWLTGVTEPIEFAFMF 324

Query: 364 IAPVLYVVYAITTGLAFALADLINLRVHAFGFIELITRTPMMVNAGLTRDLINFVIVSLV 423
           +AP+L++++ + +GLA+ +  ++++  H+  F   +    ++ +  L+R+   F ++  +
Sbjct: 325 VAPLLFLIHVMLSGLAYFVCIMLDIH-HSIVFSHGLVDFTLLFS--LSRNTGWFAVLGPL 381

Query: 424 FFGLNFTLFNFLIKKFNLPTPGRAGNYIDNEDEASEGTGNVQDGSLATKVIDLLGGKENI 483
              + + LF   I  FNL TPGR           S+GT   ++   A  +I  LGG++NI
Sbjct: 382 TAVIYYILFRGSILAFNLKTPGRL---------QSDGTKGSKESLRA--IIAALGGRDNI 430

Query: 484 ADVDACMTRLRVTVKDLDVVAPEAQWKQNGALGLIVKDKGVQAVYGPKADVLKSDIQDML 543
            +++AC+TRLR++V   ++V  + +  Q GA G+IV  KGVQ VYG KA+ L+  +Q  L
Sbjct: 431 VELNACLTRLRLSVHSPELV-NKVRLSQLGAKGVIVMGKGVQIVYGTKAETLRKVLQRYL 489


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: 616
Number of extensions: 31
Number of successful extensions: 7
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: 499
Length adjustment: 35
Effective length of query: 510
Effective length of database: 464
Effective search space:   236640
Effective search space used:   236640
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:

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