Alignments for a candidate for malEIICB in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for malEIICB in Klebsiella michiganensis M5al

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 BWI76_RS27535 BWI76_RS27535 PTS transporter subunit IIBC

Query= TCDB::Q63GK8
         (545 letters)



>FitnessBrowser__Koxy:BWI76_RS27535
          Length = 519

 Score =  217 bits (552), Expect = 1e-60
 Identities = 164/548 (29%), Positives = 273/548 (49%), Gaps = 58/548 (10%)

Query: 10  QKFGKALLVVVAVMPAAGLMISIGKLIGMSA--GDINAVHTIARVMEDIGWAIITNLHIL 67
           QKF +A++  V  +P  GL++++  ++       + + +H + +++ D  W +  NL +L
Sbjct: 13  QKFSRAMIGAVLFLPVIGLILALSSVLTNPTLISETSFLHQLGQLLGDTFWPLFGNLGLL 72

Query: 68  FAVAIGGSWAKDRAGG-AFAALLAFVLTNRITGAIFGVNAEMLADSKAKVSSVLAGDLIV 126
           F V I    AKD+    A  +++ F++         G N   L  +      +       
Sbjct: 73  FCVGISYGLAKDKKTEVALVSVMCFIM-------FLGANHSWLEHTHGLAEKING----- 120

Query: 127 KDYF----TSVLGAPALNMGVFVGIITGFLGATLYNKYYNYNKLPQALAFFNGKRFVPFV 182
            +Y+    T +LG   ++MGVF+GII G   A ++NK     +LP AL+ + G +     
Sbjct: 121 -EYYGTGQTQLLGFVVVDMGVFLGIILGCTIAWVHNKVSTI-ELPGALSMYGGAKLTLVA 178

Query: 183 VIVWSTVTAIVLSLLWPFIQSGLNEFGRWIAASKDSAPIVAPFVYGTLERLLLPFGLHHM 242
           +       AI  +  WPF+  G+      +     +A +   FVYG  E+ L+P GLHH 
Sbjct: 179 MTPVVIFYAIAFTWFWPFMTHGIAA----LTGFMKNAGVAGVFVYGFFEKFLIPTGLHHF 234

Query: 243 LTIPMNYTELGGTYTMLTGSKVGQVVAGQDPLWLAWIT--DLNNLLANGDTKAYNDLLNN 300
           +  P   T++GGT ++      GQVV+G   ++LA++   DL        T   N+ L  
Sbjct: 235 VWSPFQLTQIGGTLSV-----DGQVVSGTQAIFLAYMRHPDL--------TPVMNEAL-- 279

Query: 301 VVPARFKAGQVIGSTAALMGIAFAMFRNVDKEKRAKYKPMFLSAALAVFLTGVTEPIEFM 360
               RF   Q + +   L G + A +     EK+   K + L A +   LTG+TEPIEF 
Sbjct: 280 ----RFSQ-QGMTTIFGLAGASLAFYHTAKPEKKMMAKAILLPAIITSMLTGITEPIEFT 334

Query: 361 FMFIAPVLYVVYAITTGLAFALADLINLRV-HAFGFIE-LITRTPMMVNAGLTRDLINFV 418
           F+F++P+L+V++A  T  + A+ D+  +R   A G IE LI   P+ V+  LTR    +V
Sbjct: 335 FLFVSPLLWVIHATLTAASQAICDIFTVRPWGASGLIEFLIYNLPLPVS--LTR-WPGYV 391

Query: 419 IVSLVFFGLNFTLFNFLIKKFNLPTPGRAGN---YIDNEDEASEGTGNVQDGSLATKVID 475
           ++ +  F + + +F  L+ K NL TPGR  +    + ++ +  +  G  Q  S+  ++I+
Sbjct: 392 LIGIGQFAVYYVIFRTLVVKLNLKTPGREDDENVKLYSKADYRKKMGEPQ--SVTNEIIN 449

Query: 476 LLGGKENIADVDACMTRLRVTVKDLDVVAPEAQWKQNGALGLIVKDKGVQAVYGPKADVL 535
            LGGKENI  VD C TRLRV + ++D+V  +   K  GA G++     VQ +YG K   +
Sbjct: 450 GLGGKENIISVDNCFTRLRVAIHNMDLV-DDTILKSTGANGVVRNRNEVQVIYGVKVGQV 508

Query: 536 KSDIQDML 543
           +S +   L
Sbjct: 509 RSRVDSWL 516


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: 647
Number of extensions: 44
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: 519
Length adjustment: 35
Effective length of query: 510
Effective length of database: 484
Effective search space:   246840
Effective search space used:   246840
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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources