GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgl in Chryseobacterium viscerum 687B-08

Align β-glucosidase (Bgl;BGL-II) (EC 3.2.1.21) (characterized)
to candidate WP_103233337.1 C1634_RS05580 beta-glucosidase

Query= CAZy::AAG59831.1
         (862 letters)



>NCBI__GCF_002899945.2:WP_103233337.1
          Length = 887

 Score =  310 bits (793), Expect = 3e-88
 Identities = 260/855 (30%), Positives = 413/855 (48%), Gaps = 128/855 (14%)

Query: 40  RLGVPAVKVSDGPNGIRGNHFFMGTPAKCLPSSTALGATWDPEVVEEVGLKLLAPEAKLR 99
           RLG+P +   +  +G+      +   A   P + AL AT++PE++ +V   + A E+KLR
Sbjct: 119 RLGIPIIPFDEALHGL------VREGATAFPQAIALAATFNPELMNKVSTAI-AKESKLR 171

Query: 100 AASLVLAPTSNIQRNPLGGRSFESFSEDPYLSGIISASYVNGVQKGGIGATIKHFVGNDK 159
               +L P  N+  +   GR+ E++ EDP+L+ ++  ++V+  +  GI  T KHF+ N  
Sbjct: 172 GIRQILTPVVNLASDVRWGRTEETYGEDPFLTSVMGVNFVSSFENQGIITTPKHFLANVG 231

Query: 160 EDDRQGYDSIISERALREIYLLPFMLTQKYAAPWAIMTAYNRVNGVHVAEDPFLLKQVLR 219
           E  R  Y    S+R L E +L+PF          ++MT+YN ++G     + +LL + L+
Sbjct: 232 EGGRDSYPIHWSKRYLEETHLIPFNNAFTNGKSRSVMTSYNLLDGRPSTANHWLLTEKLK 291

Query: 220 NEWKYKGLIMSDW--FGMYSVDH------------GIKAGLD-----------LEMPG-- 252
            +W +KG ++SD    G  +V H             I AGLD           L +P   
Sbjct: 292 KDWNFKGFVISDASAVGGANVLHFTAKDYDDASAQAINAGLDVIFQTEYTHYKLFIPPFL 351

Query: 253 ---INKWRTLDLVNRTIQARKLTPRDIKDRARVVLELVKKCAQGAPEILDGDGEERTVEL 309
              I+K R  D V+R +            RA+  L L +       +I +       ++ 
Sbjct: 352 DGRISKERIDDAVSRVL------------RAKFELGLFENPYVSVQQIEE-------LKK 392

Query: 310 ESDKLLMRRIASESIVLLKNDNVLPLKPEGGAIKKIAVVGGNAKAQVLSGGGSAALKASY 369
            + K L  + A+ES VLL+N+N     P  G +KKI VVG +A    L G      K   
Sbjct: 393 LNHKPLAEKTAAESFVLLQNNN--GTLPVPGNVKKILVVGTDALDARLGGYSGPGNKK-- 448

Query: 370 FISPYDGIKAALEPHGVEVTFSEGAR-AYKTLPTLEWDLETETGERGWIGTWHTHESDDS 428
            ++  DGIK   +   +E+ +S+G     K   T+  +  +   ++G  G + ++     
Sbjct: 449 -VNILDGIKNYTKNQDIEIIYSKGIDWNIKDFTTISNEYLSSENKKGLKGIYFSNTDLKG 507

Query: 429 MTALDQPFIAPRLVDETRIFISTSY--------PKGITKRWTMRLKGYLKPREKDTNFEF 480
             A ++        DE   F  T Y        P   + RWT +L+          N++ 
Sbjct: 508 DPAFEKQ-------DEQFNFKWTLYSPDPEKLQPDHYSIRWTGKLEA-----PDSGNYQL 555

Query: 481 GLIAAGRAKLWVDGQLVIDNWTRQRRGEAFFGSGSQEETGVYLLKAGKKHEIYVEYCNVR 540
           GL      KL++DG+LVID W +         S S +   V  +K GKK++I +E+   R
Sbjct: 556 GLRGNDGFKLYLDGKLVIDQWEKL--------SYSTKTVHVDFVK-GKKYDITIEFHENR 606

Query: 541 APADGDEDEAIMDSNPGVRLGGAEVANADDLLSEAVKLASEADAVIAVVGLNADWETEGN 600
             A+ +     +  N G+        +      EA+ LA  AD ++   G++   E E  
Sbjct: 607 GEANLE-----LIWNYGLH-------DYQKDYKEALHLAQNADYIVVTAGIH---EGEFQ 651

Query: 601 DRRTLALPGRTDELVEKVAKVNSKTVVVTQAGSAI-TLPWLDSVAAVVHAWYLGNATGDA 659
           DR +L+LPG  +  + +V+K+N  T VV   GSAI T+ W D V A++  WY G   G+A
Sbjct: 652 DRASLSLPGNQESFIHEVSKLNKPTTVVLVGGSAIKTIAWKDKVGAILDVWYPGEEGGNA 711

Query: 660 IADVLFGKQNPSGKLSLTFPKRLEDVP-SHGHFGSENGKVRYAEDLFVGYKHYHHRNIEP 718
           +A  LFG +NPSGKL +TFP     +P ++ H  +  G              Y+  + EP
Sbjct: 712 VAKTLFGVENPSGKLPITFPMEEGQLPLTYNHHPTGRG------------NDYYDLSGEP 759

Query: 719 LFPFGFGLSYTTFSLSNLQLSAPVIDHATSSFSLTATLSITNTGPVTGSEVAQLYVSYPE 778
           L+PFGFGLSYTTF +S LQL        + + ++ A +++ NTG   GSEV QLYV    
Sbjct: 760 LYPFGFGLSYTTFEISGLQLDKA---KYSENDTIIAKVNVKNTGSKAGSEVVQLYVK-DL 815

Query: 779 TSELTHAPLQLRAFKKVKDLQPGETREVKLELDKYAVSYWNDRYQTWAVENGEYEIKVGN 838
            + ++   ++L+ F+K+ +LQPGE++ V +E+    + + N++ + WAVE G Y I VGN
Sbjct: 816 LATVSRPVIELKGFQKI-ELQPGESKSVTIEIPIKQLQFLNEKME-WAVEKGIYRIMVGN 873

Query: 839 SSVSKDLTLVQRFVV 853
           S  SK+L L Q   V
Sbjct: 874 S--SKNLPLKQNIEV 886


Lambda     K      H
   0.316    0.134    0.399 

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: 1833
Number of extensions: 86
Number of successful extensions: 11
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: 862
Length of database: 887
Length adjustment: 42
Effective length of query: 820
Effective length of database: 845
Effective search space:   692900
Effective search space used:   692900
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 (21.6 bits)
S2: 56 (26.2 bits)

This GapMind analysis is from Sep 24 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