GapMind for catabolism of small carbon sources

 

Aligments for a candidate for malEIICB in Pseudomonas fluorescens FW300-N2C3

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 AO356_17535 AO356_17535 PTS N-acetyl-D-glucosamine transporter

Query= TCDB::Q63GK8
         (545 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_17535 AO356_17535 PTS
           N-acetyl-D-glucosamine transporter
          Length = 571

 Score =  221 bits (562), Expect = 8e-62
 Identities = 172/536 (32%), Positives = 259/536 (48%), Gaps = 93/536 (17%)

Query: 10  QKFGKALLVVVAVMPAAGLMISIGKLIGMSAGDINAVHTIARVMEDIGWAIITNLHILFA 69
           Q+ G+AL++ +A++P AGL++ +G    +   DI  +H       D G AI  NL ++FA
Sbjct: 10  QRLGRALMLPIAILPIAGLLLRLGDTDLL---DIAIIH-------DAGQAIFANLAMIFA 59

Query: 70  VAIGGSWAKDRAGGAFAALLAFVLTNRITGAIFGVNAEMLADSKAKVSSVLAGDLIVKDY 129
           + I   +A+D  G           T  + GAI  +              V+   L V D 
Sbjct: 60  IGIAVGFARDNNG-----------TAGLAGAIGYL--------------VMIATLKVLD- 93

Query: 130 FTSVLGAPALNMGVFVGIITGFLGATLYNKYYNYNKLPQALAFFNGKRFVPFVVIVWSTV 189
                   ++NMG+  GII+G L   LYN++ +  KLP+ LAFF G+RFVP V    +  
Sbjct: 94  -------ASINMGMLAGIISGLLAGALYNRFKDI-KLPEYLAFFGGRRFVPIVTGFSAVG 145

Query: 190 TAIVLSLLWPFIQSGLNEFGRWIAASKDSAPIVAPFVYGTLERLLLPFGLHHMLTIPMNY 249
             +V  L+WP IQ G+N FG  +  S         FV+G   RLL+  GLHH+L   M +
Sbjct: 146 LGVVFGLIWPPIQQGINGFGALLMESGS----FGAFVFGVFNRLLIVTGLHHILN-NMAW 200

Query: 250 TELGGTYTMLTGSKVGQVVAGQDPLWLAWITDLNNLLANGDTKAYNDLLNNVVPARFKAG 309
              G      T    G VV G          DL+   A GD K            +F  G
Sbjct: 201 FIFGS----FTDPATGAVVTG----------DLSRYFA-GDPKG----------GQFMTG 235

Query: 310 QVIGSTAALMGIAFAMFRNVDKEKRAKYKPMFLSAALAVFLTGVTEPIEFMFMFIAPVLY 369
                   L     AM+RN   ++R     + LS AL  FLTGVTEPIEF FMF+AP+L+
Sbjct: 236 MFPVMLFGLPAACLAMYRNALPQRRKVMGGILLSMALTSFLTGVTEPIEFAFMFLAPLLF 295

Query: 370 VVYAITTGLAFALADLINLRV---HAFGFIELITRTPMMVNAGLTRDLINFVIVSLVFFG 426
           +V+A+ TG++ A+ +L+ + +    + GFI+++       N  L       V V L +  
Sbjct: 296 LVHALLTGVSMAVTNLLGIHLGFTFSGGFIDMVLGWGKSTNGWLV------VPVGLAYAA 349

Query: 427 LNFTLFNFLIKKFNLPTPGRAGNYIDNEDEASEGTGNVQDGSLATKVIDLLGGKENIADV 486
           + + +F+F I++F+L TPGR       E+  +     + +   A   I  LGG +N+  +
Sbjct: 350 IYYLVFDFCIRRFDLKTPGR-------EEVPAGDKPAIAENQRAAAYIQALGGADNLITI 402

Query: 487 DACMTRLRVTVKDLDVVAPEAQWKQNGALGLIVKDKG--VQAVYGPKADVLKSDIQ 540
            AC TRLR+ + D +  A +AQ K  GA+ ++    G  +Q V GP AD +  +I+
Sbjct: 403 GACTTRLRLDMVDRN-KASDAQLKALGAMAVVRPGNGGSLQVVVGPMADSIADEIR 457



 Score = 28.5 bits (62), Expect = 7e-04
 Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 3/65 (4%)

Query: 470 ATKVIDLLGGKENIADVDACMT-RLRVTVKDLDVVAPEAQWKQNGALGLIVKDKGV-QAV 527
           A + +D LGG++N+  ++   T RLRV + D D    E++ K  G  G+   + GV   +
Sbjct: 488 AQQWLDALGGQDNVLQLECVATSRLRVRLAD-DKGLSESRLKGLGCQGMSSLEDGVWHLL 546

Query: 528 YGPKA 532
            G KA
Sbjct: 547 LGEKA 551


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: 779
Number of extensions: 53
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: 2
Length of query: 545
Length of database: 571
Length adjustment: 36
Effective length of query: 509
Effective length of database: 535
Effective search space:   272315
Effective search space used:   272315
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, 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