Alignments for a candidate for nagEIIA in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagEIIA in Klebsiella michiganensis M5al

Align Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized)
to candidate BWI76_RS08220 BWI76_RS08220 PTS N-acetyl glucosamine transporter subunit IIABC

Query= SwissProt::P39816
         (631 letters)



>FitnessBrowser__Koxy:BWI76_RS08220
          Length = 650

 Score =  492 bits (1266), Expect = e-143
 Identities = 280/642 (43%), Positives = 387/642 (60%), Gaps = 39/642 (6%)

Query: 10  QQLGRALMTPVAVLPAAGLLLRFGDKDLLNIPIIKDAGGVVFDNLPLIFAVGVAIGLA-G 68
           Q+LGRAL  P+AVLP A LLLRFG  DLLNI  I  AGG +FDNL LIFA+GVA   +  
Sbjct: 8   QRLGRALQLPIAVLPVAALLLRFGQPDLLNISFIAQAGGAIFDNLALIFAIGVASSWSKD 67

Query: 69  GEGVAGLAAVIGYLILTVTLDNMGKLLGLQPPYEGAEHLIDMGVFGGIIIGLLAAYLYKR 128
             G A LA  +GY +LT  +  +                I+MGV  GII GL+   +Y R
Sbjct: 68  SAGAAALAGAVGYFVLTKAMVTINPA-------------INMGVLAGIITGLVGGAVYNR 114

Query: 129 FSSIELHPVLGFFSGKRFVPIITSVSSLVIGVIFSFVWPLIQNGINAASS-LIADSTVGL 187
           +S I+L   L FF GKRFVPI T    LV+  IF +VWP +QN I+A    ++    +G 
Sbjct: 115 WSGIKLPDFLSFFGGKRFVPIATGFFCLVLAAIFGYVWPPVQNAIHAGGEWIVGAGALGS 174

Query: 188 FFYATIYRLLIPFGLHHIFYTPFYFMMGEYTDPSTGNTVTGDLTRFFAGDPTAGRFMMGD 247
             +  I RLLIP GLH +  T  +F +GE+T+ + G    GD+ RF+AGD TAG FM G 
Sbjct: 175 GIFGFINRLLIPTGLHQVLNTIAWFQIGEFTN-AAGAVFHGDINRFYAGDGTAGMFMSGF 233

Query: 248 FPYMIFCLPAVALAIIHTARPEKKKMISGVMISAALTSMLTGITEPVEFSFLFVAPVLYL 307
           FP M+F LP  ALA+   A  E++ M+ G+++S A+T+ LTG+TEP+EF F+F+AP+LYL
Sbjct: 234 FPIMMFGLPGAALAMYFAAPKERRPMVGGMLLSVAITAFLTGVTEPLEFLFMFLAPLLYL 293

Query: 308 INSILAGVIFVVCDLFHVRHGYTFSGGGIDYVLNYGL---STNGWVVIPVGIVFAFIYYY 364
           +++IL G+   V     +  G++FS G IDYVL Y L   S N W++I +G+VF  IY+ 
Sbjct: 294 LHAILTGISLFVATALGIHAGFSFSAGAIDYVLMYSLPAASKNVWMLIVMGVVFFVIYFL 353

Query: 365 LFRFAILKWNLKTPGRE-------TDEDGQNEEKAPVAKDQLAFHVLQALGGQQNIANLD 417
           LF   I  +NLKTPGRE       T+E   N E+      QLA + + A+GG  N+  +D
Sbjct: 354 LFSAVIRMFNLKTPGREDKVDDVVTEEANSNTEE---GLTQLATNYIAAVGGTDNLKAID 410

Query: 418 ACITRLRVTVHQPSQVCKDELKRLGAVGVLEVN-NNFQAIFGTKSDALKDDIKTIMAGGV 476
           ACITRLR+TV   + V     KRLGA GV+++N    Q I G K++++ D++K ++A G 
Sbjct: 411 ACITRLRLTVADSALVNDAACKRLGASGVVKLNKQTIQVIVGAKAESVGDEMKKVVARGP 470

Query: 477 PATAAALD---TVTDKPLKPD------SDETFIYPIKGETVSLGDVPDQVFSEKMMGEGF 527
            A AAA      V  + +KP       + E  + PI G+ V+L  VPD+ F+ K +G+G 
Sbjct: 471 VAAAAAASHSAPVAAQAVKPQAVANAKTVEALVSPITGDIVALEQVPDEAFASKAVGDGV 530

Query: 528 AIIPSEGKVVAPADGEIVSIFPTKHAIGFMSAGGTEILIHVGIDTVKLNGEGFEAHVTSG 587
           A+ P++  VVAPA G +V IF T HA    +  G EI++H+GIDTV LNG+GF+  V  G
Sbjct: 531 AVKPTDKIVVAPAAGTVVKIFNTNHAFCLETENGAEIVVHMGIDTVALNGQGFKRLVEEG 590

Query: 588 QAVKQGELLLTFDLNYIKQHAASAITPVIFTNTSEEDLKHIQ 629
             VK GE +L  DL ++  +A S I+PV+ +N+ +     IQ
Sbjct: 591 AEVKAGEPILELDLEFLNANARSMISPVVCSNSDDYSALVIQ 632


Lambda     K      H
   0.324    0.142    0.421 

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: 1052
Number of extensions: 55
Number of successful extensions: 8
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: 631
Length of database: 650
Length adjustment: 38
Effective length of query: 593
Effective length of database: 612
Effective search space:   362916
Effective search space used:   362916
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: 41 (22.0 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:

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