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

GapMind for catabolism of small carbon sources

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

Align alpha-glucosidase (EC 3.2.1.20) (characterized)
to candidate CA265_RS02140 CA265_RS02140 glycosyl hydrolase

Query= BRENDA::Q8RDL1
         (751 letters)



>FitnessBrowser__Pedo557:CA265_RS02140
          Length = 820

 Score =  588 bits (1516), Expect = e-172
 Identities = 308/743 (41%), Positives = 443/743 (59%), Gaps = 20/743 (2%)

Query: 17  KLELRVITDKIVNIFVTDKEEKRRD-TIAIEKKKYDIPDFNVEESKDKVLVLTKDLKVEI 75
           ++E+RV++D I+ + +        D + A+ +    +  F ++E  D   + T  +  +I
Sbjct: 61  RVEVRVVSDDIIRVRLAPHGVFLDDFSYAVPEVDQKVSVFKMQEHDDHFTISTHAVTCKI 120

Query: 76  DKKTFFITFKDKDGDVINED------YGEGVKLGDSEVRCYKKLR-EDHFYGFGEKAGYL 128
           +K  F I+F D   +V+  D      + E V  G   +   KK   E++F+G G+K+G  
Sbjct: 121 EKANFHISFSDNITNVVMVDEANSMHWEENVDFGGYYIYATKKCHPEENFFGLGDKSGNF 180

Query: 129 DKKGEKFEMWNTDEFMTHNQTTKLLYESYPFFIGMNKKHTYGIFLDNSFRSFFNMGEESE 188
           + +G +FE WNTD + +       LY + PF+IG++ +  YGIF DN+F+S+F+ G E  
Sbjct: 181 NLRGRRFENWNTDAY-SFGWNQDPLYRTIPFYIGLHNQAAYGIFFDNTFKSYFDFGSEDV 239

Query: 189 EYYYFGAYGGQMNYYFIYGNDIKEVVENYTYLTGRIELPPLWALGNQQSRYSYTPQEKVL 248
               F A GG++ YY+I+G  I +VV+ Y  LTG   +PP W LG QQ R+SY P+ KV 
Sbjct: 240 NKTSFWADGGELQYYYIHGPHIMDVVKRYATLTGTHPMPPKWTLGYQQCRWSYYPETKVK 299

Query: 249 EVAKTFREKDIPCDVIYLDIDYMEGYRVFTWNKGTFKNYKEMLKNLKSMGFKVVTIVDPG 308
           E+AK FRE+ IPCD IYLDIDYM+GYR FTWNK  F + + M+K L   GFK V ++DPG
Sbjct: 300 EIAKQFRERKIPCDAIYLDIDYMDGYRCFTWNKKYFPDPRRMIKELSDDGFKTVVMIDPG 359

Query: 309 VKRDYEYFVYREGIENDYFVKDKYGITYVGKVWPGEACFPDFLQDKVRKWWGEKIANFVR 368
           +K D +Y+V++EG E  +F +        G VWPG   FPDF   KVR WWG      V 
Sbjct: 360 IKVDDDYWVFKEGKEKRFFCRRSDDYYMEGHVWPGRCQFPDFTNPKVRSWWGNLYKELVD 419

Query: 369 DGIDGIWNDMNEPAVFETPTKTMPEDNIHILDGEKISHREAHNVYANYMALATKEGLLKE 428
            G+ G WNDMNEPAVF + T   P D  H  DG + SHR+AHNVY   M  +T EGL K 
Sbjct: 420 MGVAGFWNDMNEPAVFGSGT--FPNDVRHNYDGYRGSHRKAHNVYGMQMVRSTYEGLKKL 477

Query: 429 RTNERPFILTRAAFAGIQRYAAMWTGDNRSLYEHLLMMMPMLMNVGLSGQPFAGADVGGF 488
             N+RPF +TRA ++G+QRYA++WTGDN + +EHL +       + +SG PF G D+GGF
Sbjct: 478 MRNKRPFTITRAGYSGMQRYASVWTGDNIATWEHLKIGNIQCQRLSVSGVPFCGTDIGGF 537

Query: 489 EGDCSEELFIRWIEAAVFTPFLRVHSAIGTKDQEPWSFGKKAEDIARKFIKIRYELLPYI 548
            G+   ELF RWI+   F+PF+R HSA  T ++EPWSFG+  EDI RKFI++RY L+PY+
Sbjct: 538 SGEPDGELFTRWIQLGTFSPFMRAHSAGDTAEREPWSFGEFFEDINRKFIELRYRLMPYL 597

Query: 549 YDLFYEASKKGYPVMRPLVFEYQEDENTHKIYDEFMLGQNLLIAPVYLPSKDRREVYLPS 608
           Y +F+E  + G+P++RPLV   QE+ +     DEF  G  LLI PV       R+VYLP 
Sbjct: 598 YSVFWEHHRYGFPILRPLVMLEQENISNSFRQDEFCYGDKLLICPVLEQGAISRKVYLPK 657

Query: 609 GIWYDYFMGERYEGGNYYLVEAPIDTIPVFVKEGAIIVKQKPLSYVEEDRIEEKVVEIYR 668
           G WY+++  E  +GGN Y V+A ID++P+FV+ G ++ +   + YV+E  I E V+ IY 
Sbjct: 658 GTWYNFWTNEILDGGNEYTVDAKIDSMPMFVRAGTVLPEYPVMQYVDEKSITEVVLNIYH 717

Query: 669 GN-RGRYVHYEDDGKTFDYKKGVYNLFEIEFEYFDGEIDIKFDKVHFGYEDGAKKYRFVL 727
            +       YED G TF Y++ +Y   E +F        IK ++ + G       Y F +
Sbjct: 718 SDYEVNSYMYEDHGDTFAYEQDIY--LEKKFTVKGDAQAIKVNQRNEGLY--TPNYEFYV 773

Query: 728 KNF----DEVKKVKINGEEVEEY 746
            N      +VKK+ I+ +EV+++
Sbjct: 774 CNVIGVKFQVKKIIIDNKEVKDF 796


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: 1969
Number of extensions: 125
Number of successful extensions: 4
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: 820
Length adjustment: 41
Effective length of query: 710
Effective length of database: 779
Effective search space:   553090
Effective search space used:   553090
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
the source code
instructions for running GapMind on your computer

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