Alignments for a candidate for lacZ in Pedobacter sp. GW460-11-11-14-LB5

GapMind for catabolism of small carbon sources

Alignments for a candidate for lacZ in Pedobacter sp. GW460-11-11-14-LB5

Align β-galactosidase (Gal4214-1) (EC 3.2.1.23) (characterized)
to candidate CA265_RS04025 CA265_RS04025 glycoside hydrolase family 2

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



>FitnessBrowser__Pedo557:CA265_RS04025
          Length = 1054

 Score =  805 bits (2079), Expect = 0.0
 Identities = 441/1075 (41%), Positives = 630/1075 (58%), Gaps = 53/1075 (4%)

Query: 3    MKKRTILTSIFAFISIIVFAQEKPSRNDWENPEVFQINREPARAAFLPFADEASAIADDY 62
            MK++  +     FI+  + AQ+ PS  + + PEV  +NR P RA+   F ++  A     
Sbjct: 1    MKRKLTILFTSLFIAGQISAQDLPS--ELQTPEVVSVNRLPMRASAFAFENQDLATKRAK 58

Query: 63   TRSPWYMSLDGKWKFNWSPTPDERPKDFFNTDFNTTTWKEIGVPSNWELVGYGIPIYTNI 122
             +S +++SL+G WKFNW   P +RP DF+  DF+   W    VP+NWE  GYG PIY N 
Sbjct: 59   EKSEYFLSLNGTWKFNWVKDPRKRPTDFYKLDFDDKGWDNFKVPANWETNGYGTPIYVNQ 118

Query: 123  TYPFV--------KNPPFIDHADN-PVGSYRRTFELPENWDGRRVYLHFEGGTSAMYVWI 173
             Y F          NPPF   ADN PVGSYR+   +P NW GR+V++      SA Y+W+
Sbjct: 119  PYEFAGRQLTGARMNPPFDIPADNNPVGSYRKKINIPANWSGRQVFISLGAVKSAFYIWV 178

Query: 174  NGEKVGYSQNTKSPTEFDITKYVKVGKNQVAVEVYRWSDGSYLEDQDFWRLSGIDRSVYL 233
            NG+KVGYS+++K   EFDITKYVK G+N +A++VYRWSDG+YLE QD WR+SGI+R VYL
Sbjct: 179  NGKKVGYSEDSKLAAEFDITKYVKPGENTIALQVYRWSDGTYLECQDMWRISGIEREVYL 238

Query: 234  YSTANTRIADFFARPDLDTSYKNGSLSVDIKLKNANSVAKNNQT------VEAKLVDAAG 287
            YST    I DF    +LD +Y NG L+VD+ ++N     + N +      V   LVDA G
Sbjct: 239  YSTPKLDIRDFKVIGNLDATYTNGLLNVDLAVENYKIDQRTNHSRPDSFYVALDLVDAKG 298

Query: 288  KEVF--IKTIKINLGANTVSSTTFEQMVKSPKLWNNETPNLYTLVLTLKDENGKFVETVA 345
              V+    TI+  LG N  +  +F+  + + K W+ E P LYTL +TLKD+N K +E + 
Sbjct: 299  NNVWKDATTIQKVLG-NYKTDLSFKTQISNVKNWSAEIPYLYTLYITLKDKNNKIIEVIP 357

Query: 346  TSIGFRKVELKNGQLLVNGIRIMVHGVNIHEHNPKTGHYQDEATMMKDIKLMKQLNINAV 405
              +GFR VE+K   LLVNG R+ + GVN HEHN   GH    A M KD+++MK+LN+NAV
Sbjct: 358  QRVGFRSVEIKGSDLLVNGKRVFLKGVNRHEHNATQGHTLTHADMEKDMEMMKKLNVNAV 417

Query: 406  RCSHYPNNLLWVKLCNKYGLFLVDEANIETHGMGAELQGSFDKTKHPAYLPEWKAAHMDR 465
            R SHYP +  W++LC++YGL+++DEANIE+HG    L+ +F   K      +W+  H++R
Sbjct: 418  RHSHYPPDPYWMELCDEYGLYVIDEANIESHGRYYSLETTFANDK------QWRIPHLER 471

Query: 466  IYSLVERDKNQPSIILWSLGNECGNGPVFHEAYNWIKNRDKTRLVQFEQAGEQENTDVVC 525
            I  + ERDKN  S+I WSLGNE GNG  F+EAY W+K +D  R VQ+E+A    NTD++ 
Sbjct: 472  ITRMYERDKNHASVITWSLGNEAGNGVNFYEAYQWLKGKD-FRPVQYERAESDFNTDMIV 530

Query: 526  PMYPSMEYMKEYANRKDVKRPFIMCEYSHAMGNSNGNFQEYWDIIHSSTNMQGGFIWDWV 585
            P YPS  Y+  Y+ +    RPFIM EY+H MGNS GNF+EYWD I ++  +QGGF+W+W+
Sbjct: 531  PQYPSPNYLPRYSKQDKETRPFIMSEYAHIMGNSLGNFKEYWDAIENNPKLQGGFVWEWI 590

Query: 586  DQGFEETDEAGRKYWAYGGDMG-----GQNYTNDQNFCHNGLVWPDRTPHPGAFEVKKVY 640
            DQ   +T + G++  AYGGD        +N+ +D +FC  G+V   R   P A E+KKV+
Sbjct: 591  DQAI-DTVKNGKRIMAYGGDFPLSGPVDENF-SDNDFCVKGVVTAYRGMTPMAVELKKVH 648

Query: 641  QDI--LFKGVNLDKGIIEVENGFGYTNLDKYLFKFEVLKNGLVIKSGVI-NIRLAPQSKK 697
            Q I   F G N     I V N + + ++      +E++++G VI++GV+ N+ +  +  +
Sbjct: 649  QYIKTTFNGNNQ----INVNNSYFFKDISNVQLNWELVEDGKVIENGVVSNLNVGARQTQ 704

Query: 698  QIQIELPKLTTEDGVEYLLNVFAYTKEGTELLPQNFEIAREQFSIG---ESNYFVKVAKA 754
             + +   K     G EY LNV    K     L + +E+A EQ ++    ++N +    KA
Sbjct: 705  MLSLPF-KTNYAAGKEYFLNVHYRLKTAEPFLEKGYEVAYEQIALAGTPKANVYNSNKKA 763

Query: 755  STNPIVKDSQDAITLSANGVEVTINKKTGLMQKYTSGEENYFNQMPVPNFWRAPTDNDFG 814
                 V+ + +   +  +   +T +   G +  Y S  +      P P F+RAPTDND G
Sbjct: 764  LK---VEQTAEKAVVKGSDFTITFDLIKGTLASYVSKGQELLASGPQPGFYRAPTDNDIG 820

Query: 815  NYMQVNSNVWRTVGRFSSLDSIEVKEVSTQ---TTVVAHLFLKDIASTYTITYSMDADGS 871
              +     +WR V + ++  +I+    ST       V    LK  A T T  +++ ADG+
Sbjct: 821  AGLNTKLRMWRNVYQDNNTSNIKSTINSTADGFILTVKSSLLKGDAET-TQEFNVSADGT 879

Query: 872  LTLQNSFKAGEMALSEMPRFGMLFSLKKELDNFSYYGRGPWENYQDRNTSSLKGIYESKV 931
            + + N FKA       + R G    LK +  N  +YGRGP ENY DR T+SL G Y+S V
Sbjct: 880  VKVNNQFKAVTGNYKSLMRIGNDLQLKNDYSNIQWYGRGPGENYVDRKTASLIGTYKSTV 939

Query: 932  ADQYVPYTRPQENGYKTDIRWITLTNSSGNGIEI-LGLQPLGVSALNNYPEDFDPGLTKK 990
            +DQY PY RPQE+G KTD+RW+T TN +G G+      Q L  +AL    ED DP   KK
Sbjct: 940  SDQYFPYARPQESGNKTDVRWVTFTNKAGKGLRFEFADQLLNFNALPYSVEDLDPEAEKK 999

Query: 991  QQHTNDITPRDEVIICVDLAQRGLGGDNSWGAMPHEQYQLRNKAYSYGFVIKPIK 1045
            Q H+ ++  R+++ + +D+ Q G+ G +SWG+MP  QYQ+  K Y Y + IKPIK
Sbjct: 1000 QYHSGELVKRNQIYVHMDMQQLGVQGIDSWGSMPLIQYQIPFKDYQYSYYIKPIK 1054


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: 3279
Number of extensions: 193
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: 1046
Length of database: 1054
Length adjustment: 45
Effective length of query: 1001
Effective length of database: 1009
Effective search space:  1010009
Effective search space used:  1010009
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: 58 (26.9 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