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 (Gal02II;GalB) (EC 3.2.1.23) (characterized)
to candidate Echvi_3321 Echvi_3321 Beta-galactosidase/beta-glucuronidase

Query= CAZy::AAP86765.1
         (963 letters)



>FitnessBrowser__Cola:Echvi_3321
          Length = 820

 Score =  575 bits (1481), Expect = e-168
 Identities = 333/791 (42%), Positives = 444/791 (56%), Gaps = 78/791 (9%)

Query: 181 FDDSAWQRVDLPHDWAIAGPF-----------------LADGPHGGMGRLPSWGVGWYRK 223
           FDD  W+ V +PHDWAI GPF                 +A    G  G LP  GVGWYR+
Sbjct: 50  FDDREWESVQVPHDWAIYGPFDESNDLQIVAVTQNGEKVATKKTGRTGGLPYMGVGWYRR 109

Query: 224 ALQIPASDRGRS-LFLDLDGAMSYATVWLNGKLVGGWPYGYTSWRVDLTPYV-VPGGHNQ 281
           A ++P  D  +  + L  DGAMS A V++NG+ VG WPYGY S+  D+T ++   G  NQ
Sbjct: 110 AFEVPGFDPEKQRVKLIFDGAMSEAQVYVNGEKVGFWPYGYNSFYFDVTDFLHADGTKNQ 169

Query: 282 LTIRLDNPPDSARWYPGGGLYRNVWLTKTGPLRVAQWGTQLSTPQVSAERAQVQLAVQLD 341
           L +RL+N P S+RWYPG GLYRNV +  T  + V  WGT ++TP VS E A V +  +L+
Sbjct: 170 LAVRLENKPQSSRWYPGAGLYRNVHVLVTPKIHVPVWGTFVTTPYVSEEYASVNIKTELE 229

Query: 342 NAGAAPVQAQVSTALYALDDASGLRRGPAVAQIAAVQVQVAAGGNARVQGSTQIEAPRRW 401
           +         + T++  L        G  VA+   VQ          ++    ++ P  W
Sbjct: 230 HVSEG-TDISIETSILDLS-------GKVVAKKKNVQ---RLNHGRPLEQFLTVDHPELW 278

Query: 402 GPPPTQQPHRYVAVTEVSQGGRVVDRVETPFGVRSVVFDPDKGLVINGEHVPIRGVNNHH 461
            P   + PH YVA + +S  GR +D   T FG+R + F  DKG  +NG+    +GVN HH
Sbjct: 279 SP---ESPHLYVAKSVISIEGREIDEFTTRFGIRKIEFIADKGFFLNGQRRKFQGVNLHH 335

Query: 462 DLGALGAAFNVRAAERQLQLLQQMGANAIRMSHNPPAPELLELTDRMGLLVVDEVFDSWE 521
           DLG LGAA N  A +RQLQL++ MGA+AIR SHN PAPEL+EL D MGL+V+ E FD W+
Sbjct: 336 DLGPLGAAVNRSAIKRQLQLMKDMGADAIRTSHNMPAPELVELCDEMGLMVMVESFDEWD 395

Query: 522 MKKTPLDFHLIFPQWHEPDLRAMLRRDRNHPSIILWSVGNEVGEQYTGEAGAAIARRLHA 581
           + K    +H  F  W E DL  M+R  RNHPS+++WS+GNEV  Q + + G  +A+ L  
Sbjct: 396 VAKCKNGYHRFFDDWAEKDLVNMVRHYRNHPSVVMWSIGNEVPTQCSAD-GYQVAKFLQD 454

Query: 582 IVHAEDPTRPATAAMNYASPEMP--LPAALDVISLNYQGEGIRDTPEFEGTERIRKPPQY 639
           I H EDPTR  TA M+  S  +     A +DV   NY                  +  +Y
Sbjct: 455 ICHREDPTRLVTAGMDQISCVLDNGFAAMIDVTGFNY------------------RTHRY 496

Query: 640 PAFHAKFPRKAILSSETASALSSRGVYLFPVSAQSSAPVRDGRGGDSVAH---QVSAYEL 696
              + K P   +L SET S +SSRGVY FPV             G  V H   Q SAY L
Sbjct: 497 EEGYQKLPHSLVLGSETGSTVSSRGVYHFPVEK-----------GAQVIHENQQSSAYGL 545

Query: 697 HAVDFGSSADKVFAALDRHPFVAGEFVWTGFDYLGEPTPY----YSSRSSYSGILDLAGF 752
               + +  +  FA  D   +  G+FVWTGFDYLGEPTPY    + + SS  GI+DLAG 
Sbjct: 546 EYCSWSNLPEDDFALADDFDWTLGQFVWTGFDYLGEPTPYDTDAWPNHSSMFGIVDLAGI 605

Query: 753 PKDRYWLYQARWRPELPMAHLLPHWSWPGREGQVTPVHVFTSGDEAELFVNGVSQGRKRK 812
           PKDRY+LY++ W+PE    H+LPHW+W GREGQ TP+ V+T+   AELF+NG SQG++ K
Sbjct: 606 PKDRYYLYKSVWKPEEETLHILPHWNWEGREGQKTPLFVYTNYPSAELFINGESQGKQTK 665

Query: 813 ---APLQ--YRLRWDAVVYQPGELRVQAYKH-GRPWASDRVQTAGRATRMQLSADRNQIR 866
                LQ  YRL W   +Y+PGE++V AY   G+  A   + TAG+   ++L  +  +I 
Sbjct: 666 HKEGTLQERYRLMWMDAIYEPGEVKVVAYDSLGKKAAEKILHTAGKPHHIELVPENKRIA 725

Query: 867 GDGKDLSFITVRLLDADGRPAPTAGDRLRFRVEGAGELVATDNGDPTNLEAFVLPERNAF 926
            +G +L+FI V+++D +GR  PT    L F V GAG   A  NGDP +LE F  P+   F
Sbjct: 726 VEGDELAFIRVQVVDKEGRVCPTDQRSLSFDVAGAGAFRAVANGDPGSLELFHEPQMKVF 785

Query: 927 NGLCLVIVRAK 937
           NG   +IV AK
Sbjct: 786 NGQLTLIVSAK 796


Lambda     K      H
   0.319    0.135    0.420 

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: 2000
Number of extensions: 108
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: 963
Length of database: 820
Length adjustment: 43
Effective length of query: 920
Effective length of database: 777
Effective search space:   714840
Effective search space used:   714840
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: 56 (26.2 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