GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treEIIA in Escherichia coli BW25113

Align trehalose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate 1937187 b3947 fused predicted PTS enzymes: Hpr component/enzyme I component/enzyme IIA component (NCBI)

Query= reanno::pseudo3_N2E3:AO353_15995
         (844 letters)



>FitnessBrowser__Keio:1937187
          Length = 833

 Score =  356 bits (914), Expect = e-102
 Identities = 237/694 (34%), Positives = 365/694 (52%), Gaps = 40/694 (5%)

Query: 179 PNGLHARPAAVFAQAAKGFAASICLH--KQQDSANAKSLVAIMALQTVHGDALQVSAVGE 236
           PNG+HARPA+        F++ I  H  +     NAKS +A++   T+ GD  Q+   G 
Sbjct: 12  PNGVHARPASHVETLCNTFSSQIEWHNLRTDRKGNAKSALALIGTDTLAGDNCQLLISGA 71

Query: 237 DAELAISTLAQLLADGCGEAVTPVAVVAP------VVEAQEVSTKLLRGVCASAGSAFGY 290
           D + A   L+Q L D       P+A V         V    ++ +++R     +GSA G 
Sbjct: 72  DEQEAHQRLSQWLRDEFPHCDAPLAEVKSDELEPLPVSLTNLNPQIIRARTVCSGSAGGI 131

Query: 291 VVQVAERTLE----MPEFAADQQLERESLERALMHATQALQ-RLRDNAAGEAQADIFKAH 345
           +  ++   L     +P  A     E+ +LE  L    + ++ RL D+    A + I +AH
Sbjct: 132 LTPISSLDLNALGNLPA-AKGVDAEQSALENGLTLVLKNIEFRLLDSDG--ATSAILEAH 188

Query: 346 QELLEDPSLLEQAQALIAEGKSAAFAWNSATEATATLFKSLGSTLLAERALDLMDVGQRV 405
           + L  D SL E   A ++ G S A A  ++       F    S+ L ERALD+ DV  ++
Sbjct: 189 RSLAGDTSLREHLLAGVSAGLSCAEAIVASANHFCEEFSRSSSSYLQERALDVRDVCFQL 248

Query: 406 LKLILGVP--DGVWELPDQAILIAEQLTPSQTAALDTGKVLGFATVGGGATSHVAILARA 463
           L+ I G        +L   AI +A++LTPSQ   LD   + G     GG TSH  ILAR+
Sbjct: 249 LQQIYGEQRFPAPGKLTQPAICMADELTPSQFLELDKNHLKGLLLKSGGTTSHTVILARS 308

Query: 464 LGLPAVCGLPLQVLSLASGTRVLLDADKGELHLDPAVSVIEQLHAKRQQQRQRHQHELEN 523
             +P + G+ +  L+      + +D + G + ++P  +V     A+  QQ  R Q  L  
Sbjct: 309 FNIPTLVGVDIDALTPWQQQTIYIDGNAGAIVVEPGEAV-----ARYYQQEARVQDALRE 363

Query: 524 AARA-----AVTRDGHHFEVTANVASLAETEQAMSLGAEGIGLLRSEFLYQQRSVAPSHD 578
             R      A T DG   E+ AN+A   E + A   GAEG+GL R+E LY  R+ AP   
Sbjct: 364 QQRVWLTQQARTADGIRIEIAANIAHSVEAQAAFGNGAEGVGLFRTEMLYMDRTSAPGES 423

Query: 579 EQAGTY-SAIARALGPQRNLVVRTLDVGGDKPLAYVPMDSEANPFLGMRGIRLCLERPQL 637
           E    +  A+  A G  R+++VRT+D+GGDKP+ Y+ + +EANPFLG R +R+  E   L
Sbjct: 424 ELYNIFCQALESANG--RSIIVRTMDIGGDKPVDYLNIPAEANPFLGYRAVRIYEEYASL 481

Query: 638 LREQFRAILSSAGLARLHIMLPMVSQLSELRLARLMLEEEALALGLRELP-----KLGIM 692
              Q R+IL ++    L IM+PM+S + E+   +  L E    L    +P     +LGIM
Sbjct: 482 FTTQLRSILRASAHGSLKIMIPMISSMEEILWVKEKLAEAKQQLRNEHIPFDEKIQLGIM 541

Query: 693 IEVPAAALMADLFAPEVDFFSIGTNDLTQYTLAMDRDHPRLASQADSFHPSVLRLIASTV 752
           +EVP+   + D    E+DFFSIG+NDLTQY LA+DRD+ ++    +S +P+ LR +   V
Sbjct: 542 LEVPSVMFIIDQCCEEIDFFSIGSNDLTQYLLAVDRDNAKVTRHYNSLNPAFLRALDYAV 601

Query: 753 KAAHAHGKWVGVCGALASETLAVPLLLGLGVDELSVSVPLIPAIKAAIREVELSDCQAIA 812
           +A H  GKW+G+CG L ++   +PLL+GLG+DELS+S P IPA KA + +++  +C+ + 
Sbjct: 602 QAVHRQGKWIGLCGELGAKGSVLPLLVGLGLDELSMSAPSIPAAKARMAQLDSRECRKLL 661

Query: 813 HQVLGLESAEQVREALS----VQQQAMVETSQVL 842
           +Q +   ++ +V   L+     QQ A + T++ +
Sbjct: 662 NQAMACRTSLEVEHLLAQFRMTQQDAPLVTAECI 695


Lambda     K      H
   0.318    0.132    0.370 

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: 1240
Number of extensions: 53
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: 844
Length of database: 833
Length adjustment: 42
Effective length of query: 802
Effective length of database: 791
Effective search space:   634382
Effective search space used:   634382
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 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