Alignments for a candidate for lacZ in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for lacZ in Echinicola vietnamensis KMM 6221, DSM 17526

Align β-galactosidase (Gal4214-1) (EC 3.2.1.23) (characterized)
to candidate Echvi_2143 Echvi_2143 Beta-galactosidase/beta-glucuronidase

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



>FitnessBrowser__Cola:Echvi_2143
          Length = 1036

 Score =  731 bits (1887), Expect = 0.0
 Identities = 407/1052 (38%), Positives = 604/1052 (57%), Gaps = 32/1052 (3%)

Query: 6    RTILTSIF-AFISII-VFAQEKPSRNDWENPEVFQINREPARAAFLPFADEASAIADDYT 63
            ++I+TS+F AFI +I V  Q++ +   +ENP V + NR P RA++ P+ +EA A   +  
Sbjct: 2    KSIITSLFCAFICVIKVSGQDRKADPIFENPHVQEENRLPMRASYFPYENEALAEKGEKA 61

Query: 64   RSPWYMSLDGKWKFNWSPTPDERPKDFFNTDFNTTTWKEIGVPSNWELVGYGIPIYTNIT 123
             S  +  L+G WKF W+    + PKDF+ T F+   W +  VP+NWE  GYG PIY N  
Sbjct: 62   ASDRFFDLNGTWKFFWTDHYTKLPKDFYATGFDDAAWDDFQVPANWEFNGYGTPIYVNHP 121

Query: 124  YPFV---KNPPFIDHADNPVGSYRRTFELPENWDGRRVYLHFEGGTSAMYVWINGEKVGY 180
            + F     NPPFI++  NP G YRR   LP+ W+ ++V++H     SA  +++NG  VG 
Sbjct: 122  FEFAVDNPNPPFIENEKNPAGVYRRKISLPDGWEDQQVFIHLGAVKSAFRLYVNGVYVGL 181

Query: 181  SQNTKSPTEFDITKYVKVGKNQVAVEVYRWSDGSYLEDQDFWRLSGIDRSVYLYSTANTR 240
             +++K  +EF++T YV+ G+N + +EV RW DGSYLE QDFWR+SGI+R VYLYS     
Sbjct: 182  GEDSKLESEFELTDYVQPGENLITIEVRRWHDGSYLEAQDFWRISGIERDVYLYSRPKVH 241

Query: 241  IADFFARPDLDTSYKNGSLSVDIKLKNANSVAKNNQTVEAKLVDAAGKEVFIKTIKINLG 300
              D F +  L  SY++G L V + L N     +   TV AKL+D  G  VF +T +  +G
Sbjct: 242  FYDLFVKSPLTNSYRDGKLDVTVDLWNRTDEQQGENTVMAKLLDPNGNVVFEQT-QATIG 300

Query: 301  ANTVSSTT---FEQMVKSPKLWNNETPNLYTLVLTLKDENGKFVETVATSIGFRKVELKN 357
                   T   F   + S K W+ ETP LY L L L +  G+ +E V  ++GFR  E+  
Sbjct: 301  LKRKQGKTVLNFATEIPSVKAWSAETPTLYQLELVLANAAGEPLEVVRQNVGFRTYEVVG 360

Query: 358  GQLLVNGIRIMVHGVNIHEHNPKTGHYQDEATMMKDIKLMKQLNINAVRCSHYPNNLLWV 417
             Q LVNG  ++  GVN HE +P+T H   +  M  D+++MK+LN+NAVR SHYPN+  W 
Sbjct: 361  NQFLVNGKAVLFKGVNRHESHPETHHVITKEQMETDVRIMKELNMNAVRLSHYPNDPYWY 420

Query: 418  KLCNKYGLFLVDEANIETHGMGAELQGSFDKTKHPAYLPEWKAAHMDRIYSLVERDKNQP 477
            +LC+KYG +++DEANIE+HGM       +   +     PEW  AHM RI  +V RDKN P
Sbjct: 421  ELCDKYGFYVIDEANIESHGM------YYSPERTLGNAPEWLHAHMLRIKRMVFRDKNHP 474

Query: 478  SIILWSLGNECGNGPVFHEAYNWIKNRDKTRLVQFEQAGEQENTDVVCPMYPSMEYMKEY 537
            S++ WS+GNE GNG  F++AY WIK  D +R VQ+E++  + NTD++ P YP    M  Y
Sbjct: 475  SVVAWSMGNEAGNGYNFYKAYEWIKAYDPSRPVQYERSTYEWNTDIIVPQYPHPNSMIRY 534

Query: 538  ANRKDVKRPFIMCEYSHAMGNSNGNFQEYWDIIHSSTNMQGGFIWDWVDQG-FEETDEAG 596
            A   + KRP+IM EY+HAMGNS GNF+EYW++I +   +QGG+IWDWVDQG ++E D  G
Sbjct: 535  A-ESNPKRPYIMSEYAHAMGNSMGNFREYWEVIKAYPMLQGGYIWDWVDQGIYKEID--G 591

Query: 597  RKYWAYGGDMGGQNYTNDQNFCHNGLVWPDRTPHPGAFEVKKVYQDILFKGVNLDKGIIE 656
            ++ + YGGD G +   +D NF  NG++  DR  +P A+EV++V+Q++ F+    D+  +E
Sbjct: 592  KRVFGYGGDWGPEGTPSDDNFLINGVIMADRRWNPHAYEVRRVHQEVSFELTEDDR--LE 649

Query: 657  VENGFGYTNLDKYLFKFEVLKNGLVIKSGVI-NIRLAPQSKKQIQIELP-KLTTEDGVEY 714
            + N + + +L  Y F+  +LKNG VIK   I    LAP  ++   ++LP  L  ++  EY
Sbjct: 650  IFNEYFFRDLSNYTFEAILLKNGEVIKRASIGTFALAP--RQHTVVDLPFGLVRDESAEY 707

Query: 715  LLNVFA-YTKEGTELLPQNFEIAREQFSIGESNYFVKVAKASTNPIVKDSQDAITLSANG 773
             L V     +E   + P+   +A  +F++ +     K    + +  V++    + +S   
Sbjct: 708  RLQVEGRIVQEEGRMAPKTL-LAEAEFALTDP-VLKKFDPQAADVEVREEAGKLWISNKK 765

Query: 774  VEVTINKKTGLMQKYTSGEENYFNQMPVPNFWRAPTDNDFGNYMQVNSNVWRTVGRFSSL 833
              V  N  TG    Y  G+       P  + +R   DNDFG      S +    G+ +SL
Sbjct: 766  FSVFFNVATGQFHDYKVGKNTLIVDGPSLSLFRPLVDNDFGGGR--GSKLDYQHGKVTSL 823

Query: 834  DSIEVKEVSTQTTVVAHLF-LKDIASTYTITYSMDADGSLTLQNSFKAGEMALSEMPRFG 892
              +E +  +  T  V  ++ +    +++   Y  D  G + + N+FKA +     + + G
Sbjct: 824  QKLEHQAAADGTYQVKAIYEVLGGDASFEQVYRFDDGGKIRVDNTFKAIKGDHDYLLKIG 883

Query: 893  MLFSLKKELDNFSYYGRGPWENYQDRNTSSLKGIYESKVADQYVPYTRPQENGYKTDIRW 952
                L   LD F +YGRGPWE+Y DR  S+  G+YE  V +QY PY RPQE+G KTD+RW
Sbjct: 884  TDLKLPGALDQFKWYGRGPWESYADRKYSAQVGLYEGSVMEQYHPYVRPQESGNKTDVRW 943

Query: 953  ITLTNSSGNGIEILGLQP-LGVSALNNYPEDFDPGLTKKQQHTNDITPRDEVIICVDLAQ 1011
             +++ S   G+ I  L+  L VSAL    +   PG  K+  H+ ++ P     + VDL Q
Sbjct: 944  ASVSKSQNEGLMIYALEDLLNVSALPYGIDQLYPGKEKQNIHSGELEPNGYTNLHVDLEQ 1003

Query: 1012 RGLGGDNSWGAMPHEQYQLRNKAYSYGFVIKP 1043
             G+ G NSWG++  E Y++  K Y++ +VI P
Sbjct: 1004 TGVAGINSWGSIALEAYRVSFKDYAFSYVIAP 1035


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: 3085
Number of extensions: 175
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: 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