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 Z (LacZ;TmLac;TM1193) (EC 3.2.1.23) (characterized)
to candidate 352820 BT3293 beta-galactosidase (NCBI ptt file)

Query= CAZy::AAD36268.1
         (1087 letters)



>FitnessBrowser__Btheta:352820
          Length = 1421

 Score =  681 bits (1758), Expect = 0.0
 Identities = 395/1035 (38%), Positives = 582/1035 (56%), Gaps = 81/1035 (7%)

Query: 7    EWENPQLVSEGTEKSHASFIPYLDPFSGEWEYPEE---FISLNGNWRFLFAKNPFEVPED 63
            EW N  +     E++    IP+ D         EE   + +LNG W+F +  +P + P+D
Sbjct: 29   EWSNELVSGVNKEEAVQIAIPFTDEQQAMNLTIEESPYYKTLNGIWKFHWVADPKDRPQD 88

Query: 64   FFSEKFDDSNWDEIEVPSNWEM------KGYGKPIYTNVVYPF--------------EPN 103
            F   ++D S WD I+VP+ W++      K + KP+Y NV+YPF              +P 
Sbjct: 89   FCKPEYDVSQWDNIKVPATWQIEAVRHNKNWDKPLYCNVIYPFCEWDWKKIQWPNVIQPR 148

Query: 104  PP--FVPKDDNPTGVYRRWIEIPEDWFKKEIFLHFEGVRSFFYLWVNGKKIGFSKDSCTP 161
            P         NP G YRR   +P+ W  ++IF+ F GV + FY+WVNGKK+G+S+DS  P
Sbjct: 149  PSNYTFATMPNPVGSYRREFILPDSWKGRDIFIRFNGVEAGFYIWVNGKKVGYSEDSYLP 208

Query: 162  AEFRLTDVLRPGKNLITVEVLKWSDGSYLEDQDMWWFAGIYRDVYLYALPKFHIRDVFVR 221
            AEF LT  L+ GKN++ VEV +++DGS+LE QD W F+GI+RDV+L++ PK  IRD F R
Sbjct: 209  AEFNLTPYLKAGKNVLAVEVYRFTDGSFLECQDFWRFSGIFRDVFLWSAPKTQIRDFFFR 268

Query: 222  TDLDENYRNGKIFLDVEMRNLGEEEEKDLEVTLITPDGDEKTLVKETVKPEDRVLSFAFD 281
            TDLD+ Y+N  + LD+++       E  ++VT    D + K +  +  +         F+
Sbjct: 269  TDLDKEYKNASVSLDIDITGKRSNNEIQVKVT----DQNGKEIATQNARAVTGTNKLQFE 324

Query: 282  VKDPKKWSAETPHLYVLKLKLGE-----DEKKVNFGFRKIEI-KDGTLLFNGKPLYIKGV 335
            V +P KW+AETP+LY L + L +     D + V  GFRKIE+ +DG LL NGK    KGV
Sbjct: 325  VVNPLKWTAETPNLYNLTILLKQKGKTVDIRSVKVGFRKIELAQDGRLLINGKSTLFKGV 384

Query: 336  NRHEFDPDRGHAVTVERMIQDIKLMKQHNINTVRTSHYPNQTKWYDLCDYFGLYVIDEAN 395
            +RH+   + G  V+ E M +D++LMK  NIN VRTSHYPN   +YDLCD +G+YV+ EAN
Sbjct: 385  DRHDHSSENGRTVSKEEMEKDVQLMKSLNINAVRTSHYPNNPYFYDLCDRYGIYVLSEAN 444

Query: 396  IESHGIDWDPEVTLANRWEWEKAHFDRIKRMVERDKNHPSIIFWSLGNEAGDGVNFEKAA 455
            +E HG+     + L++   W KA  +R + MV R KNH SI+ WSLGNE+G+G+NF+ AA
Sbjct: 445  VECHGL-----MALSSEPSWVKAFTERSENMVRRYKNHASIVMWSLGNESGNGINFKSAA 499

Query: 456  LWIKKRDNTRLIHYEGTTRRGESYYVDVFSLMYPKM--------DILLEYASKKREKPFI 507
              +KK D+TR  HYE     G S Y DV S MYP +        + L ++ + +  KP +
Sbjct: 500  EAVKKLDDTRPTHYE-----GNSSYCDVTSSMYPDVQWLESVGKERLQKFQNGETVKPHV 554

Query: 508  MCEYAHAMGNSVGNLKDYWDVIEKYPYLHGGCIWDWVDQGIRKKDENGREFW-AYGGDFG 566
            +CEYAHAMGNS+GN K+YW+  E+YP L GG IWDWVDQ I+    +G  ++ A+GGDFG
Sbjct: 555  VCEYAHAMGNSIGNFKEYWETYERYPALVGGFIWDWVDQSIKMPAPDGSGYYMAFGGDFG 614

Query: 567  DTPNDGNFCINGVVLPDRTPEPELYEVKKVYQNVKIRQVSKDTYEVENRYLFTNLEMFDG 626
            DTPNDGNFC NGV+  DRT   + YEVKK++Q V +  +   TY++ N+     L+   G
Sbjct: 615  DTPNDGNFCTNGVIFSDRTYSAKAYEVKKIHQPVWVEAMGNGTYKLTNKRFHAGLDDLYG 674

Query: 627  AWKIRKDGEVIEEKTF-KIFAEPGEKRLLKI---PLPEMDDSEYFLEISFSLSEDTPWAE 682
             ++I +DG+V+      ++     + +++ I    + ++  +EYF++  F   +DT W +
Sbjct: 675  RYEIEEDGKVVFSANLEELSLNAQDSKVITIADNQINKIPGAEYFIKFRFCQKQDTEWEK 734

Query: 683  KGHVVAWEQFLLKAPAFEKKSISDG-VSLREDGKHLTVEAKDTVYVFSKLTGLLEQILHR 741
             G+ VA EQF L   A       +G + L E      V+       FSK  G +      
Sbjct: 735  AGYEVASEQFKLSDSAKPVFKAGEGSIDLIETDDAYLVKGSQFEASFSKQQGTISSYTLN 794

Query: 742  RKKILKSPVVPNFWRVPTDNDIGNRMPQRLAIW-KRASKERKLFKMHW--KKEENRVSVH 798
               ++   +  N +R PTDND      Q    W ++   +  L   HW  +KE+N+V++ 
Sbjct: 795  ELPMISKGLELNAFRAPTDND-----KQVDGDWYQKGLYQMTLEPGHWNVRKEDNKVTLQ 849

Query: 799  SVFQLPGNS-WVYTT---YTVFGNGDVLVDLSLIPAEDVPEIPRIGFQFTVPEEFGTVEW 854
                  G + + Y T   YTV  +G +LV+ ++IP+     IPRIG++  +PE F  + W
Sbjct: 850  IENLYRGKTGFDYRTNIEYTVAADGSILVNSTIIPSTKGVIIPRIGYRMELPEGFERMRW 909

Query: 855  YGRGPHETYWDRKESGLFARYRKAVGEMMHRYVRPQETGNRSDVRWFALS--DGETKLFV 912
            YGRGP E Y DRK++     Y + V +    YVR QE GNR D+RW +++  DG   +F+
Sbjct: 910  YGRGPLENYVDRKDATYVGVYDELVSDQWVNYVRAQEMGNREDLRWISITNPDGIGFVFI 969

Query: 913  SGMPQIDFSVWPFSMEDL------ERVQHISELPERDFVTVNVDFRQMGLGGDDSWGAMP 966
            +G  ++  S    + +D+       R+ H  E+P R    + +D  Q  L G+ S G  P
Sbjct: 970  AG-DKMSASALHATAQDMVDPANHRRLLHKYEVPMRKETVLCLDANQRPL-GNASCGPGP 1027

Query: 967  HLEYRLLPKPYRFSF 981
              +Y L  +P  FSF
Sbjct: 1028 MQKYELRSQPTVFSF 1042


Lambda     K      H
   0.319    0.139    0.438 

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: 4611
Number of extensions: 256
Number of successful extensions: 13
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: 1087
Length of database: 1421
Length adjustment: 48
Effective length of query: 1039
Effective length of database: 1373
Effective search space:  1426547
Effective search space used:  1426547
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 (21.7 bits)
S2: 59 (27.3 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