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 α-glucosidase II / oligo-α-1,6-glucosidase (BthG II) (EC 3.2.1.10|3.2.1.20) (characterized)
to candidate CA265_RS13795 CA265_RS13795 alpha-glycosidase

Query= CAZy::BAA76396.1
         (787 letters)



>FitnessBrowser__Pedo557:CA265_RS13795
          Length = 817

 Score =  330 bits (847), Expect = 1e-94
 Identities = 234/771 (30%), Positives = 372/771 (48%), Gaps = 57/771 (7%)

Query: 31  FSHTEHVFSFHCDTGIVKIRFYREDIVRIAFNPFGETSLSTSVAVVKEP-EKVDASVHET 89
           F  T +  SF    G VK  F   +I RI  +  G+   + ++ V+      V   V + 
Sbjct: 31  FKKTGNTISFSTTRGEVKFEFCTPEIFRIRSSWSGKFEANENLMVINYSLANVAVKVSDK 90

Query: 90  EEEVTLTSAKQTVVLQKRPFRVRIYDNHGRLLVAEGKKGMAFTYQGEVCCFKMMDEADHF 149
           ++   L +AK  V L K PFR+ ++D  G+LL +E  KG       +V   K +   +HF
Sbjct: 91  KDHFLLATAKLVVKLYKAPFRIDVFDAKGKLLSSE-LKGAVSKENTQVGVSKKLQADEHF 149

Query: 150 YGFGEKTGFLDKRGETMTM-WNTDVYAPHNPETDPLYQSH----PYFMTVRNGSAHGIFF 204
           +GFGE+  F+D+R + +T+        PH      + +++    P+FM+ +    +GIFF
Sbjct: 150 FGFGERMDFMDRRFKKLTLNVGRGKGLPHAIGAYNILEANYCPVPFFMSTKG---YGIFF 206

Query: 205 DNTYKTTFDF-QTATDEYCFSAEGGAIDYYVFAGPTPKDVLEQYTDLTGRMPLPPKWALG 263
            N++ T +D   T  D+Y F A  G +DYY   GPT   +L+ YT +TG+ P+ P++ALG
Sbjct: 207 HNSFATEWDMGATKKDQYSFKAADGELDYYFMYGPTFPAILDHYTSITGKSPMLPQFALG 266

Query: 264 YHQSRYS--------YETEQEVREIAQTFIEKDIPLDVIYLDIHYM-----NGYRVFTFD 310
            H   YS          ++  V E+A+ +    IP+D+++LD  +       G    +F+
Sbjct: 267 LHAGTYSGGTWGHEAQSSDHYVVELAKKYRSLGIPVDLLWLDSTWRLFGENGGKGATSFE 326

Query: 311 -RNRFPNLKQLIADL-----KQKGIRVVPIVDPGVKEDPEYVIYQEGIRHDYFCKYIEGN 364
            R  F + K +   +     K  G+ + P  D   K +      ++G  +    K     
Sbjct: 327 WRETFKDPKSMFDSIYAMNYKMVGLHLRPRFDNAKKLNLLDQAREKGYTYPENGK----- 381

Query: 365 VYFGEVWPGKSAFPDFTNKKVRKWWGEKHQF-YTDLGIEGIWNDMNEPSVFNETKTMDVK 423
                  PG+  F +F ++K  +WW +        LG + +  D  E S F        K
Sbjct: 382 -------PGE--FVNFFDEKATQWWWDNGVMRVAKLGAKFLKTD--EGSAFGSLANESEK 430

Query: 424 VIHDNDGDPKTHRELHNVYGFMMGEATYKGMKKLLNGKRPFLLTRAGFSGIQRYAAVWTG 483
           V        K    LHN++     +A +   ++  NG R    TR G+SGIQRY  ++ G
Sbjct: 431 V----GPTGKDAERLHNLFPIAYAKAPFLEFER-FNGFRGLNQTREGYSGIQRYPYIFAG 485

Query: 484 DNRSFWEHLQMSLPMCMNLGLSGVAFCGPDVGGFAHNTNGELLTRWMQVGAFTPYFRNHC 543
           D  S W++    +   +N+GLSGV      +GGF H  + EL  RW+Q G F+P      
Sbjct: 486 DWPSEWQYFAPVIKAGLNVGLSGVGSWAHCMGGFEHQADPELYIRWVQFGMFSPIALVFG 545

Query: 544 AIGFRRQEPWAFGEKYERIIKKYIRLRYQWLPHLYTLFAEAHETGAPVMRPLFFEYPDDE 603
                 +EPW +GE   R  KKY  LRY+  P+LYT   + +ETG P+MR L   + DDE
Sbjct: 546 MDHPGYKEPWKYGEDALRNFKKYDLLRYRLFPYLYTSMHQQYETGLPMMRALVLNHQDDE 605

Query: 604 NTYNLYDEFLVGANVLIAPIMTPSTTRRVAYFPKGNWVDYWTGEVLEGGQYHLISADLET 663
           N Y + D+++ G ++++AP+ T     R  Y P+G W +YWT E  EG  YH + A L+T
Sbjct: 606 NVYEIGDQYMFGDHLMVAPVTTKGAITRSVYLPEGTWFNYWTNEKYEGKSYHHVVAPLDT 665

Query: 664 LPIFIKQGSAIAL-GDVKRSTEMPDEHRTVHIYKANGGKATYVLYDDDGQTFSYEKGDY- 721
           +P+F+K GS I +  ++  S E P +  T+ ++    G++ Y LY+DD  + +Y+ G + 
Sbjct: 666 IPLFVKAGSIIPMQPEMTYSGEKPVDVITLDVFPY--GESKYDLYEDDNLSAAYKTGSFA 723

Query: 722 LRMYIEVEYGENSVHIVTKSEGTYQPS-WKLSFAIHHATEQTKVTIDGNEQ 771
           L     +    N    V K  G+++PS  K    IH   +    T+  N Q
Sbjct: 724 LTKITSLLTASNFTLRVAKPAGSFKPSKHKYLAKIHWTGKADPATVSENGQ 774


Lambda     K      H
   0.321    0.138    0.434 

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: 1860
Number of extensions: 105
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 787
Length of database: 817
Length adjustment: 41
Effective length of query: 746
Effective length of database: 776
Effective search space:   578896
Effective search space used:   578896
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:

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