Alignments for a candidate for lacZ in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments for a candidate for lacZ in Sphingomonas koreensis DSMZ 15582

Align beta-galactosidase (EC 3.2.1.23) (characterized)
to candidate Ga0059261_2643 Ga0059261_2643 Beta-galactosidase

Query= BRENDA::B9LW38
         (700 letters)



>FitnessBrowser__Korea:Ga0059261_2643
          Length = 687

 Score =  370 bits (951), Expect = e-107
 Identities = 225/620 (36%), Positives = 312/620 (50%), Gaps = 45/620 (7%)

Query: 3   LGVCYFPEHWPSEEWERDVAAMADAGLEYVRMAEFSWGVLEPERGTFDFEWLDEAIELIG 62
           +GV ++PE WP + W  D+  M  +G   VR+ EF+W  +EPE G FDF W+D AI    
Sbjct: 39  VGVAWYPEQWPEDRWAVDLDMMKASGFNTVRIGEFAWARMEPEEGKFDFAWMDRAIAAAV 98

Query: 63  DHGMQAVLCTPTATPPKWLVDERPSIRQEDPDGTVREHGSRRHYCFNSDAYREETARIVE 122
             G   V+ TP+A PP WL    P   + D +G    HG RRH+ F S  YRE + RI  
Sbjct: 99  KRGFMVVIGTPSAAPPAWLTQNYPDTLRVDENGQRASHGGRRHFSFASRRYRELSRRIAV 158

Query: 123 RVTERYADSPHVAGWQTDNEFGCHETVRCYCDDCADAFRTWLADRYGDIDRLNEAWGNAF 182
            +  RY   P V GWQ DNE G       +  +   A+  +L  RYG ID LN  W   +
Sbjct: 159 EMATRYGKHPSVVGWQVDNEVG----PPSWDAESVAAWHAFLKQRYGTIDALNRRWTTQY 214

Query: 183 WSQQYGSFDEIDPPGPTPAEHHPSRLLAYARFSSDSVVEYNRLHADLIRE-ADPDWFVTH 241
           WSQ Y  + +I  P     + +P  LL +  F++    +Y +  A  IR   D   ++T 
Sbjct: 215 WSQFYNDWSQI--PLRQTGQQNPGLLLDFRHFTTAVWTDYIQNQARAIRPLIDRRAWITT 272

Query: 242 NFMGRFPTLNAYDVSEDLDRVAWDSYPTGFVQDRYDGEASPDQLRAGDPDQV--GMDHDI 299
           N M      + + +  DLD  +WD+Y              PD    G PD V  G +H +
Sbjct: 273 NTMFWNAGFDHFVMHRDLDLASWDNY-------------IPD----GRPDWVANGANHAL 315

Query: 300 YRSALDRPFWVMEQQPGDVNWPPHCPQPGEGAMRLWAHHAAAHGADAVLYFRWRRCLEGQ 359
            R    R FW+ME QPG V+W P       G +R  A  + +HG+D VLY++WR    GQ
Sbjct: 316 VRGYKQRNFWLMETQPGRVDWVPVNRALDPGQVRELAWQSVSHGSDGVLYWQWRPARNGQ 375

Query: 360 EQYHAGLRKADGSPDRGYADAAHTSEEF---ATLDGASHVDAPVAVVFDYDSLWALNAQP 416
           E YH  +   DG P+  +A+    ++E    A L   +   A VA+++ YDS WA++ Q 
Sbjct: 376 ETYHGAVLGQDGEPNPIHAEITQIAKELTAAAPLLADTGPAAKVAMLWSYDSRWAIDLQR 435

Query: 417 HAPDFDYWALQEAFYGAVRGRGVQVDVVPPSADLSGYAAVVAPALHLVTEDLADRLTDYI 476
           H  DFD        Y  +R +   V VV P A L+ Y  VVAP L++VT+  ADRL  Y+
Sbjct: 436 HHRDFDPVKAFTDVYRPLRVQSQGVHVVSPDAALAAYPLVVAPNLNVVTQAQADRLAAYV 495

Query: 477 AGGGEVLFGPRTGVKDAENKLRPMSQPGPLTDLVGATVDQHESLPRRLETTVRRVGDPTD 536
            GGG ++ GPR+G+KD  N L P  QPGPL+DL+GA V+Q+ +L             P  
Sbjct: 496 RGGGHLVLGPRSGMKDDANALWPQRQPGPLSDLLGAMVEQYYALDA-----------PVG 544

Query: 537 DSEEIAAPPVSFRTWAEWLDPDAAEPQYA---YDVDGPADGRPAVVTNTVGDGQVTYCGV 593
              E+    V+   WAE + PDA + +      D  G  DG+PA VT  VG G +TY G 
Sbjct: 545 IKGELGKGKVAI--WAEEIRPDAVDVRVIATYTDPGGWLDGKPAAVTRKVGRGSITYFGA 602

Query: 594 WPESDLADALASDLLDRAGV 613
           W +    + LA+ LL  A +
Sbjct: 603 WLDPATMNTLAARLLGEAKI 622


Lambda     K      H
   0.318    0.137    0.444 

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: 1658
Number of extensions: 98
Number of successful extensions: 6
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: 700
Length of database: 687
Length adjustment: 39
Effective length of query: 661
Effective length of database: 648
Effective search space:   428328
Effective search space used:   428328
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 (21.7 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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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