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

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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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources