GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ptsG-crr in Klebsiella michiganensis M5al

Align PTS system glucoside-specific EIICBA component; EIICBA-Glc 2; EC 2.7.1.- (characterized)
to candidate BWI76_RS08220 BWI76_RS08220 PTS N-acetyl glucosamine transporter subunit IIABC

Query= SwissProt::Q53922
         (692 letters)



>FitnessBrowser__Koxy:BWI76_RS08220
          Length = 650

 Score =  451 bits (1161), Expect = e-131
 Identities = 265/692 (38%), Positives = 398/692 (57%), Gaps = 71/692 (10%)

Query: 10  GQLQRIGKALMLPVAILPAAGILLTFGNAMHNEQILHFAPWMQHHYIQLISQIMEASGQV 69
           G  QR+G+AL LP+A+LP A +LL FG       +L+            IS I +A G  
Sbjct: 5   GFFQRLGRALQLPIAVLPVAALLLRFG----QPDLLN------------ISFIAQAGG-A 47

Query: 70  IFDNLPLLFAMGTALGLA-GGDGVAGIAALVGYLIMSATMGKIAGITIDDIFSYADGAKT 128
           IFDNL L+FA+G A   +    G A +A  VGY +++  M     +TI+           
Sbjct: 48  IFDNLALIFAIGVASSWSKDSAGAAALAGAVGYFVLTKAM-----VTIN----------- 91

Query: 129 LGQSAKDPAHALVLGIPTLQTGVFGGIIIGALAAWCYNKFYNIQLPQFLGFFAGKRFVPI 188
                           P +  GV  GII G +    YN++  I+LP FL FF GKRFVPI
Sbjct: 92  ----------------PAINMGVLAGIITGLVGGAVYNRWSGIKLPDFLSFFGGKRFVPI 135

Query: 189 ITSLVAIVTGIVLSFVWPPVQDGLNNLSNFLLGKNLALTTFIFGIIERSLIPFGLHHIFY 248
            T    +V   +  +VWPPVQ+ ++    +++G   AL + IFG I R LIP GLH +  
Sbjct: 136 ATGFFCLVLAAIFGYVWPPVQNAIHAGGEWIVGAG-ALGSGIFGFINRLLIPTGLHQVLN 194

Query: 249 APFWFEFGHYVNESGNLVRGDQRIWMAQYQDGVPFTAGAFTTGKYPFMMFGLPAAAFAIY 308
              WF+ G + N +G +  GD   + A   DG   TAG F +G +P MMFGLP AA A+Y
Sbjct: 195 TIAWFQIGEFTNAAGAVFHGDINRFYA--GDG---TAGMFMSGFFPIMMFGLPGAALAMY 249

Query: 309 RQAKPERRKVVGGLMLSAALTSFLTGITEPLEFSFLFVAPILYVAHVILAGTSFLIMHLL 368
             A  ERR +VGG++LS A+T+FLTG+TEPLEF F+F+AP+LY+ H IL G S  +   L
Sbjct: 250 FAAPKERRPMVGGMLLSVAITAFLTGVTEPLEFLFMFLAPLLYLLHAILTGISLFVATAL 309

Query: 369 HVQIGMTFSGGFIDYILYGLLSWDRSNALLVIPVGIAYALIYYFLFTFLIKKLNLKTPGR 428
            +  G +FS G IDY+L   L     N  ++I +G+ + +IY+ LF+ +I+  NLKTPGR
Sbjct: 310 GIHAGFSFSAGAIDYVLMYSLPAASKNVWMLIVMGVVFFVIYFLLFSAVIRMFNLKTPGR 369

Query: 429 EDK-------EVESK-DVSVSELPFEVLEAMGNKDNIKHLDACITRLRVEVRDKGLVDVE 480
           EDK       E  S  +  +++L    + A+G  DN+K +DACITRLR+ V D  LV+  
Sbjct: 370 EDKVDDVVTEEANSNTEEGLTQLATNYIAAVGGTDNLKAIDACITRLRLTVADSALVNDA 429

Query: 481 KLKQLGASGVLEVG-NNMQAIFGPKSDQIKHDMQQIM-DGKITSPAETTVTEDGDVETAE 538
             K+LGASGV+++    +Q I G K++ +  +M++++  G + + A  + +     +  +
Sbjct: 430 ACKRLGASGVVKLNKQTIQVIVGAKAESVGDEMKKVVARGPVAAAAAASHSAPVAAQAVK 489

Query: 539 IVAEGGA----VIYAPITGEAVDLSEVPDKVFSAKMMGDGIAIKPETGEVVAPFDGKVKM 594
             A   A     + +PITG+ V L +VPD+ F++K +GDG+A+KP    VVAP  G V  
Sbjct: 490 PQAVANAKTVEALVSPITGDIVALEQVPDEAFASKAVGDGVAVKPTDKIVVAPAAGTVVK 549

Query: 595 IFPTKHAIGLESKDGIELLIHFGLETVKLDGEGFEILVKENDNIVLGQPLMKVDLNYIKE 654
           IF T HA  LE+++G E+++H G++TV L+G+GF+ LV+E   +  G+P++++DL ++  
Sbjct: 550 IFNTNHAFCLETENGAEIVVHMGIDTVALNGQGFKRLVEEGAEVKAGEPILELDLEFLNA 609

Query: 655 HADDTITPIIITNAGSANIEVLH-TGKVEQGE 685
           +A   I+P++ +N+   +  V+  TGKV  G+
Sbjct: 610 NARSMISPVVCSNSDDYSALVIQATGKVVAGQ 641


Lambda     K      H
   0.323    0.142    0.417 

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: 1064
Number of extensions: 50
Number of successful extensions: 6
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: 692
Length of database: 650
Length adjustment: 39
Effective length of query: 653
Effective length of database: 611
Effective search space:   398983
Effective search space used:   398983
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (25.4 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