GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lacL in Bacteroides thetaiotaomicron VPI-5482

Align β-galactosidase L+M (LacL+LacM) (EC 3.2.1.23) (characterized)
to candidate 352867 BT3340 beta-galactosidase (NCBI ptt file)

Query= CAZy::AAA25267.1
         (626 letters)



>lcl|FitnessBrowser__Btheta:352867 BT3340 beta-galactosidase (NCBI
           ptt file)
          Length = 1036

 Score =  407 bits (1047), Expect = e-118
 Identities = 236/618 (38%), Positives = 334/618 (54%), Gaps = 34/618 (5%)

Query: 10  DPEVFRVNQLPAHSDHHYYHDTAEFKTGSRF----IKSLNGAWRFNFAKTPAERPVDFYQ 65
           DPEV  VN+   H+++  Y    E K GS+       +LNG W+FN+ +    RP +FYQ
Sbjct: 29  DPEVNSVNRSAMHTNYFAYASADEAKAGSKEDSQNFMTLNGLWKFNWVRNADARPTNFYQ 88

Query: 66  PDFDATDFDTIQVPGHIELAGYGQIQYINTLYPWEGKIYRRPPYTLNQDQLTPGLFSDAA 125
             F+   +D I+VP   EL GYG   Y+N  Y W  +    PP       L P       
Sbjct: 89  TSFNDKGWDNIKVPAVWELNGYGDPIYVNVGYAWRNQFQNNPP-------LVP-----TE 136

Query: 126 DNTVGSYLKTFDLDDVFKGQRIIIQFQGVEEALYVWLNGHFIGYSEDSFTPSEFDLTPYI 185
           +N VGSY K   L   +KG+ I   F  V   +Y+W+NG ++GYSEDS   +EFDLT Y+
Sbjct: 137 NNHVGSYRKEIVLPADWKGKDIFAHFGSVTSNMYLWVNGRYVGYSEDSKLEAEFDLTNYL 196

Query: 186 QDQGNVLAVRVYKHSTAAFIEDQDMFRFSGIFRDVNILAEPASHITDLDIRPVPNANLKS 245
           +   N++A +V++    +++EDQD FR+SG+ RD  + A     I D+ + P  ++  K 
Sbjct: 197 KPGKNLIAFQVFRWCDGSYLEDQDFFRYSGVGRDCYLYARDKKRIQDIRVTPDLDSQYKD 256

Query: 246 GELNITTKVTGEPATLALTVKDHDGRVLTSQTQTGSGSVTFDTMLFDQLHLWSPQTPYLY 305
           G LNI   + G   T+AL + D  G+ + +    GSG +   T+       W+ +TP LY
Sbjct: 257 GTLNIAIDMKGS-GTVALDLTDAQGKSVATADLKGSGKLN-TTINVANPAKWTAETPNLY 314

Query: 306 QLTIEVYDADHQLLEVVPYQFGFRTVELRDDKVIYVNNKRLVINGVNRHEWNAHTGRVIS 365
            LT  + +    + EV+P + GFR +EL   +++ VN + ++  G +RHE +   G V+S
Sbjct: 315 TLTATLKNGS-TVTEVIPVKVGFRKIELTGGQIL-VNGQPVLFKGADRHEMDPDGGYVVS 372

Query: 366 MADMRADIQTMLANNINADRTCHYPDQLPWYQLCDEAGIYLMAETNLESHGSWQKMGAIE 425
           +  M  DI+ M   NINA RTCHYPD   WY LCD+ G+Y++AE N+ESHG    MG  +
Sbjct: 373 LERMIQDIKVMKQLNINAVRTCHYPDDNRWYDLCDQYGLYVVAEANVESHG----MGYGD 428

Query: 426 PSYNVPGDNPHWPAAVIDRARSNYEWFKNHPSIIFWSLGNESYAGEDIAAMQAFYKEHDD 485
            S      NP +  A ++R + N +   NHPSIIFWSLGNE+  G +      + K  D 
Sbjct: 429 KSL---AKNPIYAKAHMERNQRNVQRGYNHPSIIFWSLGNEAGMGPNFEHCYTWIKNEDK 485

Query: 486 SRLVHYEGVFYTPELKDRISDVESRMYEKPQNIVAYLEDNPTKPFLNCEYMHDMGNSLGG 545
           +R V YE            +D+   MY    N + Y E N  KP + CEY H MGNS GG
Sbjct: 486 TRAVQYEQAG-----TSEFTDIFCPMYYDYNNCIKYCEGNIDKPLIQCEYAHAMGNSQGG 540

Query: 546 MQSYNDLIDKYPMYQGGFIWDFIDQALFVHDPITDQDVLRYGGDFDERH-SDYAFSGNGL 604
            + Y D+  KYP YQGGFIWDF+DQ+    +      +  YGGDF++   SD  F+ NGL
Sbjct: 541 FKEYWDITRKYPKYQGGFIWDFVDQSCHWKNK-DGVAIYGYGGDFNKYDASDNNFNDNGL 599

Query: 605 MFADRTPKPAMQEVKYYY 622
           +  DR P P   EV Y+Y
Sbjct: 600 ISPDRVPNPHAYEVGYFY 617


Lambda     K      H
   0.320    0.138    0.430 

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: 1899
Number of extensions: 107
Number of successful extensions: 9
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: 626
Length of database: 1036
Length adjustment: 41
Effective length of query: 585
Effective length of database: 995
Effective search space:   582075
Effective search space used:   582075
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: 56 (26.2 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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