GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treC in Phaeobacter inhibens BS107

Align trehalose-6-phosphate hydrolase (TreC) (EC 3.2.1.93) (characterized)
to candidate GFF775 PGA1_c07890 putative alpha-glucosidase AglA

Query= CAZy::AAC77196.1
         (551 letters)



>FitnessBrowser__Phaeo:GFF775
          Length = 552

 Score =  297 bits (761), Expect = 6e-85
 Identities = 180/508 (35%), Positives = 268/508 (52%), Gaps = 48/508 (9%)

Query: 5   PHWWQNGVIYQIYPKSFQDTTGSGTGDLRGVIQHLDYLHKLGVDAIWLTPFYVSPQVDNG 64
           P WW+  VIYQIYP+S+QD+ G G GDLRG+ Q L ++  LGVDAIW++PF+ SP  D G
Sbjct: 17  PDWWRGAVIYQIYPRSYQDSNGDGIGDLRGITQRLPHIASLGVDAIWISPFFTSPMKDFG 76

Query: 65  YDVANYTAIDPTYGTLDDFDELVTQAKSRGIRIILDMVFNHTSTQHAWFREA-LNKESPY 123
           YDV++Y  +DP +G+L +FD+LV  A   G+R+++D+V +HTS QHAWF E+  ++++  
Sbjct: 77  YDVSDYCDVDPMFGSLSNFDQLVAAAHRLGLRVMIDLVLSHTSDQHAWFGESRQSRDNAR 136

Query: 124 RQFYIWRDGEPE-TPPNNWRSKFGGSAWRWHAESEQYYLHLFAPEQADLNWENPAVRAEL 182
             +Y+W D +P+ TPPNNW S FGGSAW+W    EQYYLH F   Q DLN+ +PAV+  L
Sbjct: 137 ADWYVWADPQPDGTPPNNWLSIFGGSAWQWDPRREQYYLHNFLVSQPDLNFHSPAVQDAL 196

Query: 183 KKVCEFWADRGVDGLRLDVVNL------ISKDPRFPEDLDGDGRRFYTDGPRAHEFLHEM 236
             V  FW +RGVDG RLD +N       +  +P  P +     +R  T  P  + + H+ 
Sbjct: 197 LDVTRFWLERGVDGFRLDTINFYYHDAELRSNPALPPE-----QRNATIAPSVNPYNHQE 251

Query: 237 N-RDVFTPRGLMTVGEMSSTSLEHCQRYA------ALTGSELSMTFNFHHLKVDYPGGEK 289
           +      P  L  +G   +   E+  + A      A  G E+  ++   +  V      +
Sbjct: 252 HLYSKNQPENLAFLGRFRALLDEYPAKAAVGEVGDAQRGLEIMGSYTAANTGVHMCYAFE 311

Query: 290 WTLAKPDFVA--LKTLFRHWQQGMHNVAWNALFWCNHDQPRIVSRFGDEGEYRVPAAKML 347
             LAK    A  L  +F    +   N  W    + NHD  R  SR+G        A ++ 
Sbjct: 312 -LLAKDVLTASRLAEVFAEVDRVAAN-GWACWAFSNHDVIRHSSRWG----LNPAAQRLF 365

Query: 348 AMVLHGMQGTPYIYQGEEIGMTNPHFTRITDYRDVESLNMFAELRNDGRDADELLAILAS 407
             ++  ++GT  IYQGEE+G+         D +D   +  + E                 
Sbjct: 366 TTMMMCLRGTTCIYQGEELGLPEADIA-FEDLQDPYGIEFWPEF---------------- 408

Query: 408 KSRDNSRTPMQW--SNGDNAGFTAGEPWIGLGDNYQQINVEAALADDSSVFYTYQKLIAL 465
           K RD  RTPM W  SNG + GF+AG+PW+ +   +  ++V +  AD  ++ + Y++ IAL
Sbjct: 409 KGRDGCRTPMVWEPSNG-SGGFSAGKPWLPVSPEHLNLSVASQEADPDAMLHHYRRAIAL 467

Query: 466 RKQEAILTWGNYQDLLPNSPVLWCYRRE 493
           RK    L  G +  L     V +  R++
Sbjct: 468 RKAHPALAVGTHDQLRAEGNVAFFTRQD 495


Lambda     K      H
   0.320    0.136    0.448 

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: 1033
Number of extensions: 42
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 551
Length of database: 552
Length adjustment: 36
Effective length of query: 515
Effective length of database: 516
Effective search space:   265740
Effective search space used:   265740
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 (21.8 bits)
S2: 53 (25.0 bits)

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

Links

Downloads

Related tools

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