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 (BgA;XCC1256) (EC 3.2.1.23) (characterized)
to candidate 349989 BT0461 beta-galactosidase (NCBI ptt file)

Query= CAZy::AAM40554.1
         (926 letters)



>FitnessBrowser__Btheta:349989
          Length = 839

 Score =  422 bits (1085), Expect = e-122
 Identities = 271/831 (32%), Positives = 401/831 (48%), Gaps = 89/831 (10%)

Query: 157 TFQRTFAKAGKDTATAAQLAFDDSNWQQVDLPHDWAVTLPFRPEP----ISASMTEEDPA 212
           TF++ +    +D A   Q  ++D  WQ V +PHDWA+  PF  +      + +   +  A
Sbjct: 29  TFEKGWKFTREDNADFIQPDYNDIKWQSVVVPHDWAIYGPFGIDNDRQLTAIAQDGQKEA 88

Query: 213 AAHGYKALGTSFPENSVGWYRRMLQIPASDLGKRICLVFDGVFRDCVVFCNGHIVGRNAS 272
             H  +  G  F    VGWYR     P+   GK+  L+FDG      V+ NG   G    
Sbjct: 89  MEHAGRTGGLPFV--GVGWYRLNFDAPSFVKGKKATLIFDGAMSHARVYINGQEAGYWPY 146

Query: 273 GYCGFEVDLSEVLDYGKPNLIVVRVDATLGEGWFYEGAGIYRHLWLQKTDPLHVPQHGVF 332
           GY  F +D++  L  G  N + VR++       +Y GAG+YR++ L  T+  H+P  G  
Sbjct: 147 GYNTFYLDVTPYLKEGTKNTLAVRLENETESSRWYPGAGLYRNVHLVVTEDAHIPTWGT- 205

Query: 333 VRSSVQGDTATAQLSTEVRNDGTASRQCVVQARITAPYG------RIVAQAASA---AVT 383
                       QL+T V  D  A     ++  +  P G      RIV +        VT
Sbjct: 206 ------------QLTTPVVKDDYAKVN--IKTTLVVPSGKQFDAYRIVTELKDKDGKVVT 251

Query: 384 VAPGQVQ-----VVEQTVPLGQAALWSIDTPQLYTLTTSVHSAGVAVDALVTPFGVRSIA 438
               Q       +  Q + + + ALWS +TP LY   + V+   +  D   T FG+R+I 
Sbjct: 252 TDEKQGSRFDDNIFSQELVVSRPALWSPETPVLYQAVSKVYEGNILKDEYTTSFGIRTIE 311

Query: 439 FDAQRGFLLNGAPLKLHGTNNHQDHAGVGTAIPDALHAWRLRQLKSMGCNAYRSSHNPAT 498
               +GF LNG      G  NH D   +G A+ DA    ++R LK MGCNA R+SHN   
Sbjct: 312 VIPNKGFFLNGKRTSFKGVCNHHDLGPLGGAVNDAAIRRQIRILKDMGCNAIRTSHNMPA 371

Query: 499 PELLALCDRLGMFVIEET------------RRMSTDPEAMAELETMVRRGRNHPSVILWS 546
           PEL+  CD +GM V+ E+             R   D  A+ +L  ++R  RN+PSV++W 
Sbjct: 372 PELIRACDEMGMMVMAESFDEWKAMKVKNGYRHVFDEWAVKDLTNLLRHYRNNPSVVMWC 431

Query: 547 LGNEEPQQVT-ERGARIVTRMQQRVRQLDPTRPTTFAMDKG---FGDGVGQVVDVVGFNY 602
           +GNE P+Q    +G ++   +Q+   + DPTRP T  MD       + +  V+D+ GFNY
Sbjct: 432 IGNEVPEQWDGNKGPKMSYFLQELCHREDPTRPVTQGMDAPDAVVNNNMAAVMDIAGFNY 491

Query: 603 RTSQMDGFHAQYPNIPIYGSETGSTVSVRGNYQRDDTRGYTR--------AYDTDHPWWA 654
           R  +    + + P   + GSET STVS RG Y+   TR + +        +YD +   W+
Sbjct: 492 RPHKYQENYKKLPQQIVLGSETASTVSSRGVYKFPVTRQWMKKYDDHQSSSYDVESCSWS 551

Query: 655 STAEAWWSYVAQRPYIAGGFIWTGFDYRGEPTP-YNRWPNVGSQFGVLDSCGFPKDNYWY 713
           +  E  +      PY  G F+WTGFDY GEPTP Y  WP+  S FG++D  G PKD Y+ 
Sbjct: 552 NLPEDDFIQHEDLPYCIGEFVWTGFDYLGEPTPYYTDWPSHSSLFGIIDLAGLPKDRYYL 611

Query: 714 YRAQWTSE-PVLHLFPHWNWDGLLQPDDKGRV-EVWCHSNLEAVELLVNGVSQG------ 765
           YR+ W  E   LH+ PHWNW+G      +G +  V+ ++N  + EL +NG SQG      
Sbjct: 612 YRSHWNKEQETLHILPHWNWEG-----REGEITPVFVYTNYPSAELFINGKSQGKRTKDL 666

Query: 766 ---------------LQQVPAYGHVEWRVAYAPGVIEARGY-RGGKLVLTERRETVGKPA 809
                          L++   Y  +     Y PG ++   Y   GK V  +   T GKP 
Sbjct: 667 SVTIDNSADSVSIMNLKRQSRYRLMWMDTKYEPGTVKVVAYDADGKAVAEKELHTAGKPD 726

Query: 810 AIRLSCDRSALRADAEDVAVVKVEIVDAQGRLVPNADHLVHLVLRGPARLIGVGNGDPSS 869
            I L  DR+ ++AD +D++ V V +VD  G L P+A H +   ++G        NG+ +S
Sbjct: 727 HIELVADRNVIKADGKDLSFVTVRVVDRDGNLCPDASHEISFKVKGEGSYRAGANGNAAS 786

Query: 870 HEDDKAPQRKAFNGLCMALLRSTRSSGQILLQATAPGLTSAALHLQAATSA 920
            E  + P+ K F+G+  A++ ST   G+I L+AT  GL   AL +++   A
Sbjct: 787 LESFQHPKMKVFSGMMTAIVSSTEQPGKITLEATGKGLKKGALIIESCQEA 837


Lambda     K      H
   0.320    0.135    0.422 

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: 1786
Number of extensions: 99
Number of successful extensions: 11
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: 926
Length of database: 839
Length adjustment: 43
Effective length of query: 883
Effective length of database: 796
Effective search space:   702868
Effective search space used:   702868
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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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