Alignments for a candidate for lacZ in Bacteroides thetaiotaomicron VPI-5482

GapMind for catabolism of small carbon sources

Alignments for a candidate for lacZ in Bacteroides thetaiotaomicron VPI-5482

Align β-galactosidase (Gal4214-1) (EC 3.2.1.23) (characterized)
to candidate 352867 BT3340 beta-galactosidase (NCBI ptt file)

Query= CAZy::AAX48919.1
         (1046 letters)



>FitnessBrowser__Btheta:352867
          Length = 1036

 Score =  761 bits (1964), Expect = 0.0
 Identities = 426/1062 (40%), Positives = 593/1062 (55%), Gaps = 54/1062 (5%)

Query: 5    KRTILTSIFAFISIIVFAQEKPSRNDWENPEVFQINREPARAAFLPFADEASAIADDYTR 64
            K+ +L+   A + +    Q + + N+W++PEV  +NR      +  +A    A A     
Sbjct: 2    KKQLLSCCLAALGLTTAIQAQ-NFNEWKDPEVNSVNRSAMHTNYFAYASADEAKAGSKED 60

Query: 65   SPWYMSLDGKWKFNWSPTPDERPKDFFNTDFNTTTWKEIGVPSNWELVGYGIPIYTNITY 124
            S  +M+L+G WKFNW    D RP +F+ T FN   W  I VP+ WEL GYG PIY N+ Y
Sbjct: 61   SQNFMTLNGLWKFNWVRNADARPTNFYQTSFNDKGWDNIKVPAVWELNGYGDPIYVNVGY 120

Query: 125  P----FVKNPPFIDHADNPVGSYRRTFELPENWDGRRVYLHFEGGTSAMYVWINGEKVGY 180
                 F  NPP +   +N VGSYR+   LP +W G+ ++ HF   TS MY+W+NG  VGY
Sbjct: 121  AWRNQFQNNPPLVPTENNHVGSYRKEIVLPADWKGKDIFAHFGSVTSNMYLWVNGRYVGY 180

Query: 181  SQNTKSPTEFDITKYVKVGKNQVAVEVYRWSDGSYLEDQDFWRLSGIDRSVYLYSTANTR 240
            S+++K   EFD+T Y+K GKN +A +V+RW DGSYLEDQDF+R SG+ R  YLY+    R
Sbjct: 181  SEDSKLEAEFDLTNYLKPGKNLIAFQVFRWCDGSYLEDQDFFRYSGVGRDCYLYARDKKR 240

Query: 241  IADFFARPDLDTSYKNGSLSVDIKLKNANSVAKNNQTVEAKLVDAAGKEVFIKTIKINLG 300
            I D    PDLD+ YK+G+L++ I +K + +VA +       L DA GK V    +K   G
Sbjct: 241  IQDIRVTPDLDSQYKDGTLNIAIDMKGSGTVALD-------LTDAQGKSVATADLK---G 290

Query: 301  ANTVSSTTFEQMVKSPKLWNNETPNLYTLVLTLKDENGKFV-ETVATSIGFRKVELKNGQ 359
            +  +++T     V +P  W  ETPNLYTL  TLK  NG  V E +   +GFRK+EL  GQ
Sbjct: 291  SGKLNTTI---NVANPAKWTAETPNLYTLTATLK--NGSTVTEVIPVKVGFRKIELTGGQ 345

Query: 360  LLVNGIRIMVHGVNIHEHNPKTGHYQDEATMMKDIKLMKQLNINAVRCSHYPNNLLWVKL 419
            +LVNG  ++  G + HE +P  G+      M++DIK+MKQLNINAVR  HYP++  W  L
Sbjct: 346  ILVNGQPVLFKGADRHEMDPDGGYVVSLERMIQDIKVMKQLNINAVRTCHYPDDNRWYDL 405

Query: 420  CNKYGLFLVDEANIETHGMGAELQGSFDKTKHPAYLPEWKAAHMDRIYSLVERDKNQPSI 479
            C++YGL++V EAN+E+HGMG    G     K+P Y      AHM+R    V+R  N PSI
Sbjct: 406  CDQYGLYVVAEANVESHGMG---YGDKSLAKNPIY----AKAHMERNQRNVQRGYNHPSI 458

Query: 480  ILWSLGNECGNGPVFHEAYNWIKNRDKTRLVQFEQAGEQENTDVVCPMYPSMEYMKEYAN 539
            I WSLGNE G GP F   Y WIKN DKTR VQ+EQAG  E TD+ CPMY       +Y  
Sbjct: 459  IFWSLGNEAGMGPNFEHCYTWIKNEDKTRAVQYEQAGTSEFTDIFCPMYYDYNNCIKYC- 517

Query: 540  RKDVKRPFIMCEYSHAMGNSNGNFQEYWDIIHSSTNMQGGFIWDWVDQGFEETDEAGRKY 599
              ++ +P I CEY+HAMGNS G F+EYWDI       QGGFIWD+VDQ     ++ G   
Sbjct: 518  EGNIDKPLIQCEYAHAMGNSQGGFKEYWDITRKYPKYQGGFIWDFVDQSCHWKNKDGVAI 577

Query: 600  WAYGGDMGGQNYTNDQNFCHNGLVWPDRTPHPGAFEVKKVYQDILFKGVNLDKGIIEVEN 659
            + YGGD    +  +D NF  NGL+ PDR P+P A+EV   YQ+I     +L KG I + N
Sbjct: 578  YGYGGDFNKYD-ASDNNFNDNGLISPDRVPNPHAYEVGYFYQNIWTTPADLSKGEINIYN 636

Query: 660  GFGYTNLDKYLFKFEVLKNGLVIKSGVI-NIRLAPQSKKQIQIELPKLTTEDGVEYLLNV 718
               + +L  +  ++++L NG +I++G++ ++ +APQ   ++Q+           E LLNV
Sbjct: 637  ENFFRDLSAFYLEWQLLANGEIIQNGIVSDLNVAPQQTAKLQLPFDIKNICSCKELLLNV 696

Query: 719  FAYTKEGTELLPQNFEIAREQFSIGE-------------SNYFVKVAKASTNPIVKDSQD 765
                K    LLP    IA +Q SI +             SN  V V     N       +
Sbjct: 697  SYKLKAAETLLPAGETIAYDQMSIRDYKAPELKLENKQSSNIAVVVPSFQDN-----DHN 751

Query: 766  AITLSANGVEVTINKKTGLMQKY-TSGEENYFNQMPV-PNFWRAPTDNDFGNYMQVNSNV 823
             + +S     +  NK  G + +Y  SG +   +   + PNFWRAPTDNDFG  +Q     
Sbjct: 752  YLIVSGEDFTLEFNKHNGYLCRYDVSGTQLMEDGSALTPNFWRAPTDNDFGAGLQHRYGA 811

Query: 824  WRTVGRFSSLDSIEVKEVSTQTTVVAHLFLKDIASTYTITYSMDADGSLTLQNSFKAGE- 882
            W+       L S++    + Q  V A   +K I     +TY+++  G++ +    +A + 
Sbjct: 812  WKNPE--LKLTSLKHDIENEQAVVRAEYDMKSIGGKLFLTYAINNKGAVKVTQKMEADKS 869

Query: 883  MALSEMPRFGMLFSLKKELDNFSYYGRGPWENYQDRNTSSLKGIYESKVADQYVPYTRPQ 942
              +S+M RFGM   +    +   YYGRGP ENY DRN ++  G Y   V +Q+ PY RPQ
Sbjct: 870  KKVSDMFRFGMQLRMPVTFNEIEYYGRGPGENYSDRNHAARIGKYRQTVEEQFYPYIRPQ 929

Query: 943  ENGYKTDIRWITLTNSSGNGIEILGLQPLGVSALNNYPEDFDPGLTKKQQHTNDITPRDE 1002
            E G KTDIRW  L N  GNG++ +   P   SALN   E  D G  K Q+H+ ++   + 
Sbjct: 930  ETGTKTDIRWWRLLNIGGNGLQFVADAPFSASALNYTIESLDDGAGKDQRHSPEVEKANF 989

Query: 1003 VIICVDLAQRGLGGDNSWGAMPHEQYQLRNKAYSYGFVIKPI 1044
               C+D  Q GL   NSWGA+  E+Y+L  + Y + F++ P+
Sbjct: 990  TNFCIDKVQTGLACVNSWGAIALEKYRLPYQDYEFSFIMNPV 1031


Lambda     K      H
   0.316    0.134    0.410 

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: 3250
Number of extensions: 195
Number of successful extensions: 12
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: 1046
Length of database: 1036
Length adjustment: 45
Effective length of query: 1001
Effective length of database: 991
Effective search space:   991991
Effective search space used:   991991
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 57 (26.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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