Aligments for a candidate for treP in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Aligments for a candidate for treP in Escherichia coli BW25113

Align alpha,alpha-trehalose phosphorylase (EC 2.4.1.64) (characterized)
to candidate 15436 b1316 predicted hydrolase (NCBI)

Query= BRENDA::D6XSD4
         (757 letters)



>lcl|FitnessBrowser__Keio:15436 b1316 predicted hydrolase (NCBI)
          Length = 755

 Score =  307 bits (786), Expect = 2e-87
 Identities = 233/777 (29%), Positives = 367/777 (47%), Gaps = 81/777 (10%)

Query: 5   ISSKALDQDQLLVDESLFAQGNGYLGIRGNFEEGYAADMTTIRGAYL-NAFHDVVPIEYG 63
           +S     Q  L    SL AQGNGYLG+R + EE Y       RG YL   +H     E  
Sbjct: 7   LSEPHFSQHTLNKYASLMAQGNGYLGLRASHEEDYTRQT---RGMYLAGLYHRAGKGEIN 63

Query: 64  EKLFGFPDTQQKLVNNIDVQSIRIIIDGDDFSLFQGEILDFERFLYMKDGYSERRIHWKS 123
           E           LVN  DV  + I I+G+ FSL       ++R L    G   R + W++
Sbjct: 64  E-----------LVNLPDVVGMEIAINGEVFSLSHEA---WQRELDFASGELRRNVVWRT 109

Query: 124 PAGKEVSIHFYRMISFTDKELFVQWIDIEPISQVQEIEIVSTVDGDVSNFVEASDPRVAS 183
             G   +I   R +S     L    I I P+            D D S  +        +
Sbjct: 110 SNGSGYTIASRRFVSADQLPLIALEITITPL------------DADASVLISTGIDATQT 157

Query: 184 GHAKR-LHVTDVQDKGPY-MQVSDETEVSKLKVSATTWVSASREALKESRSSFEGKVEER 241
            H ++ L  T V+  G + MQ S  T+  +  V+ +     S +  +   +     ++  
Sbjct: 158 NHGRQHLDETQVRVFGQHLMQGSYTTQDGRSDVAISCCCKVSGDVQQCYTAKERRLLQHT 217

Query: 242 RTFSGEGSLRYEKRSVYTDTYRHESSPS-----EAGFELAKRLSAVSLDELIRGQRAYLN 296
                 G     ++ V+ D +R +   +      A     +  +  S D+L+        
Sbjct: 218 SAQLHAGETMTLQKLVWID-WRDDRQAALDEWGSASLRQLEMCAQQSYDQLLAASTENWR 276

Query: 297 RFWQTSDIRIAGDDKL-QEGIRFNLYQL-LQSVGKEPTSNISAKGLSGEGYEGHYFWDTE 354
           ++WQ   I + G +   Q+ + + LY L + +   +  S+I+AKGL+GEGY+GH FWDTE
Sbjct: 277 QWWQKRRITVNGGEAHDQQALDYALYHLRIMTPAHDERSSIAAKGLTGEGYKGHVFWDTE 336

Query: 355 IYMYPPFLMTDPEIAKNLLLHRFSLLDAARERAKEMGHRQGALFPWRTI-SGGECSAFFP 413
           +++ P  L +DP +A++LL +R+  L  A+E+A+  G  QGALFPW +  SG E +  F 
Sbjct: 337 VFLLPFHLFSDPTVARSLLRYRWHNLPGAQEKARRNGW-QGALFPWESARSGEEETPEFA 395

Query: 414 A-------------GSAQYHISADIAYSFIQYYLTTGDEVFLADYGAELLVETARLWIDT 460
           A               A++H+ ADIA++ IQY+ TTGDE F+A  G  LL+ETA+ WI  
Sbjct: 396 AINIRTGLRQKVASAQAEHHLVADIAWAVIQYWQTTGDESFIAHEGMALLLETAKFWISR 455

Query: 461 GHMKDGRFRIDDVTGPDEYTCIVNNNYYTNSMAKHNLEWAVKAMALVEERHPTVYKNLAA 520
               + R  I DV GPDEYT  VNNN YT+ MA++N++ A+               N+A 
Sbjct: 456 AVRVNDRLEIHDVIGPDEYTEHVNNNAYTSYMARYNVQQAL---------------NIAR 500

Query: 521 RLAVTDDELKAFREASE----SMYYPYSDSHRIHAQDDTFLNKQVWDIEG--TPKEEFPL 574
           +   +DD   AF   +E     ++ P      +  QDD+F+ K   ++        +  +
Sbjct: 501 QFGCSDD---AFIHRAEMFLKELWMPEIQPDGVLPQDDSFMAKPAINLAKYKAAAGKQTI 557

Query: 575 LLHYHPLTLYRYQVCKQADTVLSHFLLEDEADEETIRRSYDYYEQVTTHDSSLSFCVFSI 634
           LL Y    +   Q+ KQAD V+ +++L ++    +   +  +YE  T HDSSLS  +  I
Sbjct: 558 LLDYSRAEVNEMQILKQADVVMLNYMLPEQFSAASCLANLQFYEPRTIHDSSLSKAIHGI 617

Query: 635 MAAKLGYEKKAYEYFSETARLDLDNTHKNTKDGLHMANMGGTWLALVSGFGGMRVKETGL 694
           +AA+ G   ++Y+++ E   +DL     +  DG+H A  G  WL  + GF G+ V++  L
Sbjct: 618 VAARCGLLTQSYQFWREGTEIDLGADPHSCDDGIHAAATGAIWLGAIQGFAGVSVRDGEL 677

Query: 695 HFAPRLPEAWDSLSFQIQYQGRVIALDIGRDKTVYTLTEGDVINMYHHGKLFTLTEQ 751
           H  P LPE W  LSF + +QG    L +  D     +     +++  +G+L T+ E+
Sbjct: 678 HLNPALPEQWQQLSFPLFWQG--CELQVTLDAQRIAIRTSAPVSLRLNGQLITVAEE 732


Lambda     K      H
   0.319    0.135    0.401 

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: 1319
Number of extensions: 60
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: 757
Length of database: 755
Length adjustment: 40
Effective length of query: 717
Effective length of database: 715
Effective search space:   512655
Effective search space used:   512655
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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