GapMind for catabolism of small carbon sources

 

Alignments for a candidate for susB in Echinicola vietnamensis KMM 6221, DSM 17526

Align alpha-glucosidase (EC 3.2.1.20) (characterized)
to candidate Echvi_2842 Echvi_2842 Alpha-glucosidases, family 31 of glycosyl hydrolases

Query= BRENDA::Q8RDL1
         (751 letters)



>FitnessBrowser__Cola:Echvi_2842
          Length = 808

 Score =  562 bits (1448), Expect = e-164
 Identities = 286/695 (41%), Positives = 431/695 (62%), Gaps = 12/695 (1%)

Query: 3   QRTVEGIVVRSEGKKLELRVITDKIVNIFVTDKEEKRRDTIAIEKKKYDIPDFNVEESKD 62
           ++T  GI   ++     + + T KIV + V+       +  ++     + P  N+ E  D
Sbjct: 23  EQTPHGIAGITDKAYFNICLYTAKIVRVQVSRTVPFTPNPYSVVASPEETP-VNLHEEAD 81

Query: 63  KVLVLTKDLKVEIDKKTFFITFKDKDGDVINEDYGE-GVKLGDSEVRCYKKLR-EDHFYG 120
            +++ TKDLK+ ++K  + +T+ D++G+++N+D    GV    +EV  YKKL+  + F G
Sbjct: 82  FLILETKDLKIVLNKNEWALTYYDQNGNLLNQDDPAFGVSWLGTEVTNYKKLQPHEKFIG 141

Query: 121 FGEKAGYLDKKGEKFEMWNTDEFMTHNQTTKLLYESYPFFIGMNKKHTYGIFLDNSFRSF 180
            GEK G +D+ G+ F  WNTD F  +      LY S PF+IG++++  YGIF DN+ ++ 
Sbjct: 142 LGEKTGGIDRAGQAFVNWNTDYF-AYGVNDDPLYMSIPFYIGIHQELAYGIFFDNTHKTT 200

Query: 181 FNMGEESEEYYYFGAYGGQMNYYFIYGNDIKEVVENYTYLTGRIELPPLWALGNQQSRYS 240
           FN G  +  + YF A  G M+YYF  G+ + E++  YT LTG++ LPP WALG QQ RYS
Sbjct: 201 FNFGASNRRFSYFSADDGDMDYYFFQGDSVSEIIGGYTSLTGKLALPPKWALGFQQCRYS 260

Query: 241 YTPQEKVLEVAKTFREKDIPCDVIYLDIDYMEGYRVFTWNKGTFKNYKEMLKNLKSMGFK 300
           Y P+ +V  +AKTFR+KD+P DVIYLDI +M+ Y+VFT++   F N K M+K L + GF+
Sbjct: 261 YYPESEVFTLAKTFRDKDMPADVIYLDIHHMKKYKVFTFDGEKFPNPKAMIKALNAKGFR 320

Query: 301 VVTIVDPGVKRDYEYFVYREGIENDYFVKDKYGITYVGKVWPGEACFPDFLQDKVRKWWG 360
           VV I+DPG+K + +Y  Y EG++ D F+K   G TY G+VWPG   FPDF   K R+WW 
Sbjct: 321 VVVIMDPGIKVEKDYLPYEEGMDQDLFLKYPDGETYEGQVWPGWCAFPDFTAAKTREWWA 380

Query: 361 EKIANFVRDGIDGIWNDMNEPAVFETPTKTMPEDNIHILDGEKISHREAHNVYANYMALA 420
           EK+A +   G+DG W DMNEPA +   T  +   +    +GE++SHR+A N+Y   MA A
Sbjct: 381 EKMAFYTDAGVDGFWTDMNEPASWGQHTPNLINFD---YEGEQVSHRKARNIYGMQMARA 437

Query: 421 TKEGLLKERTNERPFILTRAAFAGIQRYAAMWTGDNRSLYEHLLMMMPMLMNVGLSGQPF 480
            + G       ERPFILTRA F+GIQR+AA WTGDN +  EH+L  + ++ ++G+SG  F
Sbjct: 438 AQNG-ASTNGQERPFILTRAGFSGIQRFAAAWTGDNVASEEHMLAGIRLVNSLGISGVSF 496

Query: 481 AGADVGGFEGDCSEELFIRWIEAAVFTPFLRVHSAIGTKDQEPWSFGKKAEDIARKFIKI 540
           AG DVGGF G+ S+ LF RW+  A F P  R HS I + D EPW+FG++ E+I++ ++K+
Sbjct: 497 AGYDVGGFCGEASKSLFARWMSIAAFAPLYRAHSMINSNDAEPWAFGEEVEEISKNYLKL 556

Query: 541 RYELLPYIYDLFYEASKKGYPVMRPLVFEYQEDENTH--KIYDEFMLGQNLLIAPVYLPS 598
           RY++LP  Y  FY++++ G PV + L  +Y  D++ +  +  ++++    LL+ PV    
Sbjct: 557 RYKMLPLWYSAFYKSTQDGLPVAKSLAIDYCFDDHVYDARFQNQYICCDALLVVPVE-SH 615

Query: 599 KDRREVYLPSGIWYDYFMGERYEGGNYYLVEAPIDTIPVFVKEGAIIVKQKPLSYVEEDR 658
           K+  + YLP G WY  +  + Y+G     V+ PI+ +PVFVK G+I+  Q P+S+  E  
Sbjct: 616 KEITKAYLPEGQWYYLYNDDSYKGAQEIYVDTPINYLPVFVKGGSILPLQSPVSHTAEQH 675

Query: 659 IEEKVVEIYRG-NRGRYVHYEDDGKTFDYKKGVYN 692
                + +Y+G     Y+HYEDDG T DY+KG ++
Sbjct: 676 DGILRLHVYKGEGTSSYIHYEDDGVTLDYQKGKHH 710


Lambda     K      H
   0.320    0.141    0.426 

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: 1773
Number of extensions: 81
Number of successful extensions: 7
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: 751
Length of database: 808
Length adjustment: 41
Effective length of query: 710
Effective length of database: 767
Effective search space:   544570
Effective search space used:   544570
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: 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