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 Beta-galactosidase BoGH2A; Beta-gal; Glycosyl hydrolase family protein 2A; BoGH2A; EC 3.2.1.23 (characterized)
to candidate Echvi_1669 Echvi_1669 Beta-galactosidase/beta-glucuronidase

Query= SwissProt::A7LXS9
         (851 letters)



>FitnessBrowser__Cola:Echvi_1669
          Length = 828

 Score =  877 bits (2265), Expect = 0.0
 Identities = 431/810 (53%), Positives = 547/810 (67%), Gaps = 35/810 (4%)

Query: 35  SSSLVSPRERSDFNADWRFHLGDGLQAAQPGFADNDWRVLDLPHDWAIEGDFSQENPSGT 94
           +SS    R+  DFN  WRF LGD   A    F  ++WR L+LPHDW+IEGDFS+++P+  
Sbjct: 40  ASSEDKERQVIDFNYGWRFQLGDHPNAISEDFDVSNWRELNLPHDWSIEGDFSEDHPTKP 99

Query: 95  GGGALPGGVGWYRKTFSVDKADAGKIFRIEFDGVYMNSEVFINGVSLGVRPYGYISFSYD 154
            GGALP G+GWYRK F +      +   IEFDGVY N EV+ING  LG RP GY SF YD
Sbjct: 100 EGGALPAGIGWYRKAFKLPTEAKEQSIWIEFDGVYRNGEVWINGHRLGKRPNGYSSFKYD 159

Query: 155 LTPYLKW-DEPNVLAVRVDNAEQPNSRWYSGCGIYRNVWLSKTGPIHVGGWGTYVTTSSV 213
           L  +L + D+ NVLAVRVDN+EQPNSRWY+G GIYRNV L +TG +HV  WGTYVTT  +
Sbjct: 160 LGEHLNYGDKVNVLAVRVDNSEQPNSRWYTGSGIYRNVRLIRTGKVHVEHWGTYVTTPEI 219

Query: 214 DEKQAVLNLATTLVNESDTNENVTVCSSLQDAEGREVAETRSSGEAEAGKEVVFTQQLTV 273
            +  AV+NL   + N+      +TV S++ DA+G  V E         G+    TQ+ TV
Sbjct: 220 TDSSAVVNLEVMVKNDGFNERKLTVRSTILDADGEAVTEEEQPLVLGKGESTDVTQRFTV 279

Query: 274 KQPQLWDIDTPYLYTLVTKVMRNEECMDRYTTPVGIRTFSLDARKGFTLNGRQTKINGVC 333
             P+LW  D PYLY +VT+V    + MD Y TP+GIR F+ DA+KGF+LNG++ KI GVC
Sbjct: 280 PSPKLWSTDEPYLYQVVTQVYAGMQLMDDYVTPLGIRYFNFDAQKGFSLNGKRMKILGVC 339

Query: 334 MHHDLGCLGAAVNTRAIERHLQILKEMGCNGIRCSHNPPAPELLDLCDRMGFIVMDEAFD 393
            HHDLG LGAAVN RAIER L+ILKEMG N IR +HNPPAPELL LCD MGFIV DEAFD
Sbjct: 340 NHHDLGALGAAVNKRAIERRLEILKEMGVNAIRTAHNPPAPELLQLCDEMGFIVQDEAFD 399

Query: 394 MWRKKKTAHDYARYFNEWHERDLNDFILRDRNHPSVFMWSIGNEVLEQWSDAKADTLSLE 453
           +W+KKK   D   ++++WH RDL D ILRDRNHPS+ MWSIGNE+ EQ+           
Sbjct: 400 VWKKKKVDADSHLFWDQWHRRDLEDLILRDRNHPSIMMWSIGNEIREQF----------- 448

Query: 454 EANLILNFGHSSEMLAKEGEESVNSLLTKKLVSFVKGLDPTRPVTAGCNEP-NSGNHLFR 512
                               +S    +TK+LV  VK LD TR VT    E   S N +++
Sbjct: 449 --------------------DSTGISITKELVRIVKELDTTRVVTCALTENIPSKNFIYQ 488

Query: 513 SGVLDVIGYNYHNKDIPNVPANFPDKPFIITESNSALMTRGYYRMPSDRMFIWPKRWDKS 572
           S  LD++G+NY +KD  N P  +P +  I TE+ SAL TRG+Y +PSD +  WP+  DK 
Sbjct: 489 SKALDLLGFNYKHKDHKNFPKWYPGEKLIATENMSALATRGHYDLPSDTIMRWPQAHDKP 548

Query: 573 F--ADSTFACSSYENCHVPWGNTHEESLKLVRDNDFISGQYVWTGFDYIGEPTPYGWPAR 630
               +     S+Y+     WG+THEE+ K ++D DF++G +VWTGFDY+GEP PY +PAR
Sbjct: 549 LETGNEDLTVSAYDQVSAYWGSTHEETWKSIKDQDFMAGLFVWTGFDYLGEPIPYPYPAR 608

Query: 631 SSYFGIVDLAGFPKDVYYLYQSEWTDKQVLHLFPHWNWTPGQEIDMWCYYNQADEVELFV 690
           SSYFGIVDLAGFPKD YY+YQSEWT   VLH+FPHWNW  GQE+D+W YYNQADEVELF+
Sbjct: 609 SSYFGIVDLAGFPKDAYYMYQSEWTADTVLHVFPHWNWEAGQEVDVWAYYNQADEVELFL 668

Query: 691 NGKSQGVKRKDLDNLHVAWRVKFEPGTVKVIARESGKVVAEKEICTAGKPAEIRLTPDRS 750
           NG+S G+K+K+ D+LHV WR  FEPGT+K +AR+ GK VAEK++ TAG   ++ L+PDR 
Sbjct: 669 NGESLGIKQKEGDDLHVMWRTPFEPGTLKAVARKDGKKVAEKKVTTAGDAQKVTLSPDRK 728

Query: 751 ILTADGKDLCFVTVEVLDEKGNLCPDADNLVNFTVQGNGFIAGVDNGNPVSMERFKDEKR 810
            + ADGKDL F+TV + D  GN+ P+ADN+VNF +QG G I GVDNG   S+E FK   R
Sbjct: 729 TIKADGKDLSFITVSICDMDGNIVPNADNMVNFEIQGEGKIMGVDNGYQASLEPFKANYR 788

Query: 811 KAFYGKCLVVIQNDGKPGKAKLTATSEGLR 840
           KAF GKCL+++Q+  + G+  + ATSE L+
Sbjct: 789 KAFKGKCLLIVQSAREAGEISIRATSEHLQ 818


Lambda     K      H
   0.319    0.136    0.431 

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: 2049
Number of extensions: 97
Number of successful extensions: 5
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: 851
Length of database: 828
Length adjustment: 42
Effective length of query: 809
Effective length of database: 786
Effective search space:   635874
Effective search space used:   635874
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