Aligments for a candidate for treEIIA in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Aligments 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)



>lcl|FitnessBrowser__Keio:1937187 b3947 fused predicted PTS enzymes:
           Hpr component/enzyme I component/enzyme IIA component
           (NCBI)
          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:

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