GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutU in Pedobacter sp. GW460-11-11-14-LB5

Align Urocanate hydratase (EC 4.2.1.49) (characterized)
to candidate CA265_RS22275 CA265_RS22275 urocanate hydratase

Query= reanno::SB2B:6937476
         (670 letters)



>FitnessBrowser__Pedo557:CA265_RS22275
          Length = 668

 Score =  996 bits (2574), Expect = 0.0
 Identities = 483/666 (72%), Positives = 551/666 (82%), Gaps = 1/666 (0%)

Query: 5   MTFAEQIKQGIPAELPSPKPYPADANRAPKRKDILTAAEKQLAVRNALRYFPAEWHQELA 64
           M F  Q+  GIP+ LP+ KP   + + AP RKD+LTA EK+LAV+NALRYFP  WHQELA
Sbjct: 1   MDFKAQLLAGIPSTLPAKKPRNTELSHAPVRKDVLTADEKKLAVKNALRYFPKAWHQELA 60

Query: 65  AEFAKELNDFGRIYMYRFKPEYAMKARAISEYPAKCEQAAAIMLMVDNNLDPAVAQHPEE 124
            EF  EL ++G IYMYRF P+YA+ AR I+ YP     AAAIMLM+ NNLDPA+AQHPEE
Sbjct: 61  QEFLTELENYGHIYMYRFMPDYAIYARDIAAYPCLTVHAAAIMLMIQNNLDPAIAQHPEE 120

Query: 125 LITYGGNGAVFQNWAQYRLTMKYLSEMEADQTLHLYSGHPMGLFPSSVDAPRVVVTNGMM 184
           LITYGGNG+VFQNWAQY LTM+YL+ M   QTL++YSGHP GLFPS+  APRVVVTNGMM
Sbjct: 121 LITYGGNGSVFQNWAQYLLTMQYLATMTDQQTLNIYSGHPQGLFPSNTAAPRVVVTNGMM 180

Query: 185 IPNYSKPDDWERFNALGVTQYGQMTAGSFMYIGPQGIVHGTTITVMNGFRKVLEKGDSPK 244
           +PNYS P+D E+FNALGVTQYGQMTAGS+MYIGPQGIVHGT IT+MN FRK    G    
Sbjct: 181 VPNYSSPEDLEKFNALGVTQYGQMTAGSYMYIGPQGIVHGTAITLMNAFRKKGFYGKDTA 240

Query: 245 GKIFLTAGLGGMSGAQPKAGNIAGCITVCAEVNPKAATKRHAQGWVDELIDNMDALVARV 304
           GKIFLTAGLGGMSGAQ KAGNI GCITVCAEVNPKAATKR  QGWVDELIDN+D L+ RV
Sbjct: 241 GKIFLTAGLGGMSGAQTKAGNIVGCITVCAEVNPKAATKRQQQGWVDELIDNLDELINRV 300

Query: 305 KQAQANEEVVSIAFIGNVVNVWEAFDEHDIFVHLGSDQTSLHNPWSGGYYPVDISYDESN 364
             AQ  +E VS+A+IGN+V+VWE FD+ +I V +GSDQTSLHNP+SGGYYPV +S+ E+N
Sbjct: 301 IVAQKEKETVSLAYIGNIVDVWERFDQENIEVAIGSDQTSLHNPYSGGYYPVGLSFAEAN 360

Query: 365 RLIREEPELFKTKVQATLKRHADAINRHTAKGTYFFDYGNAFLLEASRAGGDVMAENGID 424
            ++   P  FK  VQ +LKR A +IN+HT KGTYFFDYGNAFLLE SRAG DVM+ NGID
Sbjct: 361 EMMAGAPGQFKVYVQDSLKRQAASINKHTGKGTYFFDYGNAFLLECSRAGADVMSPNGID 420

Query: 425 FKYPSYVQDILGPMCFDYGFGPFRWVCTSGNSADLDRTDAIAAEVLARIMAEAPAEIQQQ 484
           FKYPSYV+DILGP+CFDYGFGPFRWVC SGN  DLD TD +A EV+  I   APAEIQQQ
Sbjct: 421 FKYPSYVEDILGPLCFDYGFGPFRWVCASGNENDLDLTDQMAKEVMEEIKLSAPAEIQQQ 480

Query: 485 MQDNITWIKDAKQNKLVVGSQARILYADAEGRMEIAKAFNDAISRGEI-GPVVLGRDHHD 543
           +QDNI WI  AK+NKLVVGS+ARILYADAEGR +IA  FN AI  GE+  PV+LGRDHHD
Sbjct: 481 LQDNINWISAAKENKLVVGSKARILYADAEGRAKIALRFNQAIKTGELSAPVILGRDHHD 540

Query: 544 VSGTDSPFRETSNIYDGSRFTADMAIHNVIGDSFRGATWVSIHNGGGVGWGEVINGGFGM 603
           VSGTDSPFRETSNIYDGSRFTADMAIHNVIGDSFRGATWVSIHNGGGVGWGEVINGGFGM
Sbjct: 541 VSGTDSPFRETSNIYDGSRFTADMAIHNVIGDSFRGATWVSIHNGGGVGWGEVINGGFGM 600

Query: 604 LLDGTEAAERRLKSMLLFDVNNGIARRSWARNEEANFAIKREMARTPKLKVTLANSVDDD 663
           +LDGTE A  +L++ML +DVNNGIARRSWARN+EA FAI+REM RT  LK+TL N VDD+
Sbjct: 601 VLDGTEQAAEKLQNMLFYDVNNGIARRSWARNKEARFAIEREMERTGTLKITLPNLVDDE 660

Query: 664 IINGLE 669
           +++GLE
Sbjct: 661 VLDGLE 666


Lambda     K      H
   0.318    0.134    0.404 

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: 1284
Number of extensions: 46
Number of successful extensions: 2
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: 670
Length of database: 668
Length adjustment: 39
Effective length of query: 631
Effective length of database: 629
Effective search space:   396899
Effective search space used:   396899
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: 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:

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