GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Keio:15436
          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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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