Alignments for a candidate for lacZ in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for lacZ in Dinoroseobacter shibae DFL-12

Align β-galactosidase (EC 3.2.1.23) (characterized)
to candidate 3607831 Dshi_1239 Beta-galactosidase (RefSeq)

Query= CAZy::ABI35985.1
         (645 letters)



>FitnessBrowser__Dino:3607831
          Length = 635

 Score =  642 bits (1656), Expect = 0.0
 Identities = 329/618 (53%), Positives = 399/618 (64%), Gaps = 11/618 (1%)

Query: 2   LGVCYYPEHWPKERWKEDARRMREAGLSHVRIGEFAWALLEPEPGRLEWGWLDEAIATLA 61
           LGVCYYPEHWP+++W  DA RM++AGL+ VRIGEFAW+ LEP PG L + WLD AI+ LA
Sbjct: 5   LGVCYYPEHWPEDQWPRDAARMKDAGLTLVRIGEFAWSRLEPSPGDLRFDWLDRAISVLA 64

Query: 62  AEGLKVVLGTPTATPPKWLVDRYPEILPVDREGRRRRFGGRRHYCFSSPVYREEARRIVT 121
             GL+VVLGTPTATPP+W++DR+P++L VD  G+ R+FG RRHYCFS P YR EA RI  
Sbjct: 65  EAGLEVVLGTPTATPPRWMLDRHPDMLAVDARGQPRKFGSRRHYCFSHPGYRAEAARIAR 124

Query: 122 LLAERYGGLEAVTGFQTDNEYGCHDTVRCYCPRCQEAFRGWLEARYGTIEALNEAWGTAF 181
           LL ERYG    +  +Q DNEYGCHDT   Y    +  FR WL  RY + +ALN AWG  F
Sbjct: 125 LLGERYGRDPRIVAWQIDNEYGCHDTTLSYSDAARHGFRDWLAQRYQSTDALNRAWGNVF 184

Query: 182 WSQRYRSFAEVELPHLTVAEPNPSHLLDYYRFASDQVRAFNRLQVEILRAHAPGKFVTHN 241
           WS  Y  F +++LP+LTV EPNP+H L + R+ASD V AFNR QV  LR       + HN
Sbjct: 185 WSMAYDRFDQIDLPNLTVTEPNPAHALAFRRYASDMVVAFNRAQVAALRPLTDAPLI-HN 243

Query: 242 FMGFFTDLDAFALAQDLDFASWDSYPLGF-TDLMPLPPEEKLRYARTGHPDVAAFHHDLY 300
           +MG  T+ D  A+  DLD ASWDSYP+GF  D +  P + K  Y R G PD  AFHHDLY
Sbjct: 244 YMGRVTEFDHHAVGADLDIASWDSYPMGFLLDRVEAPADHKAAYLRQGDPDFQAFHHDLY 303

Query: 301 RGVGR-GRFWVMEQQPGPVNWAPHNPSPAPGMVRLWTWEALAHGAEVVSYFRWRQAPFAQ 359
           RGVGR GR+W+MEQQPGPVNWAP NP+P PGMVRLW+ EA AHGAE V +FRWRQAPFAQ
Sbjct: 304 RGVGRDGRWWIMEQQPGPVNWAPWNPAPLPGMVRLWSHEAFAHGAEAVCFFRWRQAPFAQ 363

Query: 360 EQMHAGLHRPDSAPDQGFFEAKRVAEELAALALPPVAQAPVALVFDYEAAWIYEVQPQGA 419
           EQMHAGL RPD +P  G  EA  +A +L  L     ++APVALVFDY + W +EVQPQGA
Sbjct: 364 EQMHAGLLRPDDSPAPGLEEAAALAADLPRLPDVSPSRAPVALVFDYPSQWAWEVQPQGA 423

Query: 420 EWSYLGLVYLFYSALRRLGLDVDVVPPG-ASLRGYAFAVVPSLPIVREEALEAFREAEGP 478
           ++ Y  L +  Y  LR+LGL VD++P   A L G+   +VP L  +  +        +  
Sbjct: 424 DFDYFALCFAMYRGLRKLGLSVDILPADPARLAGHDLILVPGLLHLSADMTAYLATTQAQ 483

Query: 479 VLFGPRSGSKTETFQIPKELPPGPLQALLPLKVVRVESLPPGLLEVAEGALGRFPLG-LW 537
           VL GPR+GSKT    I   LP GP    L   V  VE+LPPG    AE AL R      W
Sbjct: 484 VLVGPRAGSKTPEMSI--ALPLGPNLQGLDATVTHVETLPPG----AERALQRGGAAERW 537

Query: 538 REWVEAPLKPLLTFQDGKGALYREGRYLYLAAWPSPELAGRLLSALAAEAGLKVLSLPEG 597
            E VE   + L    +G   L R GR  YLAAWP PE  GR+L  L + AG++   +PEG
Sbjct: 538 IEAVETRAEILEETTEGAPVLIRTGRQHYLAAWPDPEAMGRILRDLCSRAGIQTTDMPEG 597

Query: 598 LRLRRRGTWVFAFNYGPE 615
           +R R  G      NY  E
Sbjct: 598 VRQRVHGHHKLVVNYSSE 615


Lambda     K      H
   0.322    0.139    0.454 

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: 1440
Number of extensions: 88
Number of successful extensions: 8
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: 645
Length of database: 635
Length adjustment: 38
Effective length of query: 607
Effective length of database: 597
Effective search space:   362379
Effective search space used:   362379
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 (21.9 bits)
S2: 54 (25.4 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)
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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