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 351154 BT1626 beta-galactosidase (NCBI ptt file)

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



>FitnessBrowser__Btheta:351154
          Length = 1022

 Score =  712 bits (1837), Expect = 0.0
 Identities = 406/1065 (38%), Positives = 582/1065 (54%), Gaps = 63/1065 (5%)

Query: 1    MNMKKRTILTSIFAFISIIVFAQEKPSRNDWENPEVFQINREPARAAFLPFADEASAIAD 60
            M +KKRT L  + A  +    AQ++P   +W++     +N+        P+AD AS I  
Sbjct: 1    MKLKKRTFLILMAALTATFASAQKQPLP-EWQSQYAVGLNKLAPHTYVWPYAD-ASDIGK 58

Query: 61   D--YTRSPWYMSLDGKWKFNWSPTPDERPKDFFNTDFNTTTWKEIGVPSNWELVGYGIPI 118
               Y +SP+YMSL+GKWKFNW   PD RPKDF+   + T  W +I VP NWE  GYG  I
Sbjct: 59   PGGYEQSPYYMSLNGKWKFNWVKNPDNRPKDFYQPSYYTGGWADINVPGNWERQGYGTAI 118

Query: 119  YTNITYPF-------VKNPPFIDHADNPVGSYRRTFELPENWDGRRVYLHFEGGTSAMYV 171
            Y N TY F        KNPP +  A+N VGSYRRTF++P +W GRRV L  EG  S  YV
Sbjct: 119  YVNETYEFDDKMFNFKKNPPLVPFAENEVGSYRRTFKVPADWKGRRVVLCCEGVISFYYV 178

Query: 172  WINGEKVGYSQNTKSPTEFDITKYVKVGKNQVAVEVYRWSDGSYLEDQDFWRLSGIDRSV 231
            W+NG+ +GY+Q +K+  E+DIT  +  G+N VA+EVYRWS G+YLE QD WRLSGI+R V
Sbjct: 179  WVNGKLLGYNQGSKTAAEWDITDVLSEGENVVALEVYRWSSGAYLECQDMWRLSGIERDV 238

Query: 232  YLYSTANTRIADFFARPDLDTS-YKNGSLSVDIKLKNANSVAKNNQTVEAKLVDAAGKEV 290
            YLYST    IAD+     LD   YK G  ++++ ++  ++ A +   +   L DA+GK V
Sbjct: 239  YLYSTPKQYIADYKVSASLDKEKYKEGIFNLEVTVEGPSATASS---IAYTLKDASGKAV 295

Query: 291  FIKTIKINLGANTVSSTTFEQMVKSPKLWNNETPNLYTLVLTLKDENGKFVETVATSIGF 350
                I I     +      E+ +   K WN E PNLYTLVL LKD  GK  E     +GF
Sbjct: 296  LQDAINIKSRGLSNFIAFDEKKIAEVKAWNAEHPNLYTLVLELKDAQGKVTELTGCEVGF 355

Query: 351  RKVELKNGQLLVNGIRIMVHGVNIHEHNPKTGHYQDEATMMKDIKLMKQLNINAVRCSHY 410
            R  E+K+G+  +NG+ ++V G N HEH+ + G    +  M +DI+LMKQ NIN VR SHY
Sbjct: 356  RTSEIKDGRFCINGVPVLVKGTNRHEHS-QLGRTVSKELMEQDIRLMKQHNINMVRNSHY 414

Query: 411  PNNLLWVKLCNKYGLFLVDEANIETHGMGAELQGSFDKTKHPAYLPE---WKAAHMDRIY 467
            P +  W +LC++YGL+++DEANIE+HGMG            PA L +   W  AHMDR +
Sbjct: 415  PTHPYWYQLCDRYGLYMIDEANIESHGMGYG----------PASLAKDSTWLTAHMDRTH 464

Query: 468  SLVERDKNQPSIILWSLGNECGNGPVFHEAYNWIKNRDKTRLVQFEQAGEQENTDVVCPM 527
             + ER KN P+I++WS GNE GNG  F   Y+W+K+ +K R VQ+E+A    NTD+ C M
Sbjct: 465  RMYERSKNHPAIVIWSQGNEAGNGINFERTYDWLKSVEKGRPVQYERAELNYNTDIYCRM 524

Query: 528  YPSMEYMKEYANRKDVKRPFIMCEYSHAMGNSNGNFQEYWDIIHSSTNMQGGFIWDWVDQ 587
            Y S++ +K Y  +KD+ RPFI+CEY HAMGNS G  +EYW++  +    QGG IWDWVDQ
Sbjct: 525  YRSVDEIKAYVGKKDIYRPFILCEYLHAMGNSCGGMKEYWEVFENEPMAQGGCIWDWVDQ 584

Query: 588  GFEETDEAGRKYWAYGGDMGGQNYTNDQNFCHNGLVWPDRTPHPGAFEVKKVYQDILFKG 647
             F E D+ G+ YW YGGD G +   +  NFC NGLV   R PHP   EVKK+YQ+I  K 
Sbjct: 585  NFREIDKDGKWYWTYGGDYGPEGIPSFGNFCGNGLVNAVREPHPHLLEVKKIYQNI--KA 642

Query: 648  VNLDKGIIEV--ENGFGYTNLDKYLFKFEVL-KNGLVIKSGVINIRLAPQSKKQIQIELP 704
               D+  ++V  +N + ++NL++Y+ ++ V  ++G V+  G   +   P +   + +   
Sbjct: 643  TLSDRKNLKVCIKNWYDFSNLNEYILRWNVKGEDGTVLAEGTKEVDCEPHATVDVTLGAV 702

Query: 705  KLTTEDGVEYLLNVFAYTKEGTELLPQNFEIAREQFSIGESNYFVKVAKASTNPIVKDSQ 764
            KL       Y LN+    KE T L+  ++E+A +QF +  +               K++ 
Sbjct: 703  KLPNTVREAY-LNLSWSRKEATPLVDTDWEVAYDQFVLAGN---------------KNTT 746

Query: 765  DAITLSANGVEVTINKKTGLMQKYTSGEENYFNQMPVPNFWRAPTDNDFGNYMQVNSNVW 824
                  A      ++K TG +   T   +         + +R  TDND  N  +  + +W
Sbjct: 747  AYRPQKAGETAFVVDKNTGALSSLTLDGKELLAAPITLSLFRPATDND--NRDRNGARLW 804

Query: 825  RTVGRFSSLDS-IEVKEVSTQTTVVAHLF--LKDIASTYTITYSMDADGSLTLQNSFKAG 881
            R  G  +     + +KE  T  TV A +              Y++D +G+L ++ +F+  
Sbjct: 805  RKAGLNNLTQKVVSLKEEKTSATVRAEILNGKGQKVGMADFVYALDKNGALKVRTTFQPD 864

Query: 882  EMALSEMPRFGMLFSLKKELDNFSYYGRGPWENYQDRNTSSLKGIYESKVADQYVPYTRP 941
               +  M R G+ F +    +  SY GRG  E Y DRN S   G+Y++ V   +  Y  P
Sbjct: 865  TAIVKSMARLGLTFRMADAYNQVSYLGRGDHETYIDRNQSGRIGLYDTTVERMFHYYATP 924

Query: 942  QENGYKTDIRWITLTNSSGNGIEILGLQPLGVSALNNYPEDFDPGLTKKQQHTNDITPRD 1001
            Q    +TD+RW  LT+ +G G+ +   +P   S +      F   L +K  H N++    
Sbjct: 925  QSTANRTDVRWAKLTDQAGEGVFMESNRPFQFSII-----PFSDVLLEKAHHINELERDG 979

Query: 1002 EVIICVDLAQRGLGGDNSW-GAMPHEQYQLRNKAYSYGFVIKPIK 1045
             + I +D  Q G+G      G +P  QY +  K  S+ F + P+K
Sbjct: 980  MITIHLDAEQAGVGTATCGPGVLP--QYLVPVKKQSFEFTLYPVK 1022


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: 3003
Number of extensions: 171
Number of successful extensions: 10
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: 1022
Length adjustment: 45
Effective length of query: 1001
Effective length of database: 977
Effective search space:   977977
Effective search space used:   977977
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