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

GapMind for catabolism of small carbon sources

Aligments 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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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, 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

GapMind for catabolism of small carbon sources