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 (BgaM) (EC 3.2.1.23) (characterized)
to candidate Echvi_1698 Echvi_1698 Beta-galactosidase/beta-glucuronidase

Query= CAZy::CAA04267.1
         (1034 letters)



>FitnessBrowser__Cola:Echvi_1698
          Length = 1080

 Score =  672 bits (1733), Expect = 0.0
 Identities = 384/1036 (37%), Positives = 556/1036 (53%), Gaps = 65/1036 (6%)

Query: 23   NPEIFQLNRSKAHALLMPYQTVEEALKNDRKSSVYYQSLNGSWYFHFAENADGRVKNFFA 82
            +P I  LNR  A      Y+  E A   DR+ S   Q LNG W FHFA N      +F+ 
Sbjct: 44   DPLITSLNRMPARTTAYSYKDAETAKIGDREES-RIQLLNGDWDFHFAMNMKEAPSDFYR 102

Query: 83   PEFSYEKWDSISVPSHWQLQGYDYPQYTNVTYPWVENEELEPPFAPTKYNPVGQYVRTFT 142
               +   WD I VPS+W+L+GYD P Y +  YP+     + PP+ P  YN VG Y RTF 
Sbjct: 103  SRVT--GWDKIEVPSNWELKGYDKPIYKSAVYPF---RPINPPYVPEDYNGVGSYQRTFE 157

Query: 143  PKSEWKDQPVYISFQGVESAFYVWINGEFVGYSEDSFTPAEFDITSYLQEGENTIAVEVY 202
             +  W+D  + + F  V SAF VW+NGEFVGY EDSF P+EF+IT YL+ GEN ++V+V 
Sbjct: 158  LEENWEDMNITLHFGAVSSAFKVWLNGEFVGYGEDSFLPSEFNITPYLRSGENVLSVQVL 217

Query: 203  RWSDASWLEDQDFWRMSGIFRDVYLYSTPQVHIYDFSVRSSLDNNYEDGELSVSADILNY 262
            RWSD S+LEDQD WR+SGI R+V+L + P++ +YDF  +++L  +Y +   S+   + N 
Sbjct: 218  RWSDGSYLEDQDHWRLSGIQREVFLMAEPKLRVYDFHWQATLAEDYTNATFSLRPKVENL 277

Query: 263  FEHDTQDLTFEVMLYDANAQEVLQAPLQTNLSVSDQRTVS-----------LRTHIKSPA 311
                  D      L+DA  + V   PL+  ++V D    S           L   +++P 
Sbjct: 278  TGERVPDSKLTAQLFDAEGKPVFATPLE--MAVEDILNESYPRLDNVKFGLLEATVENPH 335

Query: 312  KWSAESPNLYTLVLSLKNAAGSIIETESCKVGFRT--FEIKNGLMTINGKRIVLRGVNRH 369
             WS E P LYTLV+ L+ A G ++E +SCKVGFR   F+ +   + INGK   + GVNRH
Sbjct: 336  LWSDEHPYLYTLVIGLEGAKGQLLEAKSCKVGFRDIRFDPETSKLLINGKETYIYGVNRH 395

Query: 370  EFDSVKGRAGITREDMIHDILLMKQHNINAVRTSHYPNDSVWYELCNEYGLYVIDETNLE 429
            +   V+G+A +TR+D+  D+  +KQ N N +RTSHYPND  +YELC+EYG+ VIDE N E
Sbjct: 396  DHHPVRGKA-LTRQDIEEDVKTIKQFNFNTIRTSHYPNDPYFYELCDEYGILVIDEANHE 454

Query: 430  THGTWTYLQEGEQKAVPGSKPEWKENVLDRCRSMYERDKNHPSIIIWSLGNESFGGENFQ 489
            THG    L    Q         W    ++R   M +RDKNHPSII WSLGNE+  G N  
Sbjct: 455  THGIGGKLSNDTQ---------WTHAYMERVSRMVQRDKNHPSIIFWSLGNEAGRGPNHA 505

Query: 490  HMYTFFKEKDSTRLVHYEGIF-----------HHRDY------------DASDIESTMYV 526
             M  +  + D TR VHYE              +H DY            D   ++     
Sbjct: 506  AMAAWVHDVDITRPVHYEPAQGNHRAEGYIPPNHPDYPKDHAHRIQVPTDQPYVDMVSRF 565

Query: 527  KPADVERYALMNPK---KPYILCEYSHAMGNSCGNLYKYWELFDQYPILQGGFIWDWKDQ 583
             P       L+N     +P +  EYSH+MGNS GN+ + W+ F   P + GG IWD+KDQ
Sbjct: 566  YPGIFTPDLLVNQHADHRPIVFIEYSHSMGNSTGNMKELWDKFRSLPQVIGGCIWDFKDQ 625

Query: 584  ALQATAEDGTSYLAYGGDFGDTPNDGNFCGNGLIFADGTASPKIAEVKKCYQPVKWTAVD 643
             L    +DG ++ AYGGDF +  +DGNFC NG++ +DG     + E K  YQPV+ T  D
Sbjct: 626  GLLKQTDDGEAFYAYGGDFDEERHDGNFCINGIVASDGRPKAAMYECKWVYQPVEMTWED 685

Query: 644  PAKGKFAVQNKHLFTNLNAYDFVWTVEKNGELVEKHASLLNVA-PDGTDELTLSYPLYEQ 702
              +    + N+H   +L  Y F  ++ +NGE V +   L N+A   G D +    P    
Sbjct: 686  STEMTVRIHNRHADKSLEDYLFELSLLQNGERVNRR-DLPNLALAAGEDTVINLKPYLPD 744

Query: 703  ENETDEFVLTLSLRLSKDTAWASAGYEVAYEQFVLPAKAAMPSVKAAHPALTVDQNEQTL 762
                DE++  L+  LS++  WA  G+EVA +QF +  K   P   A   A  V+++   +
Sbjct: 745  LQPGDEYLAHLTFSLSEEELWAGKGHEVAQQQFQV-QKGNSPEFPAPRQAFEVEESVTNI 803

Query: 763  TVTGTNFTAIFDKRKGQFISYNYERTELLASGFRPNFWRAVTDND-LGNKLHERCQTWRQ 821
             V G  F   F K  G   SY     E ++     +F R +TDND  G K HE+ + W +
Sbjct: 804  LVKGEGFQVAFGKSTGALESYQLAGEEQISQPMALSFSRPLTDNDRKGWKPHEKLKVWYE 863

Query: 822  ASLEQHVKKVTVQPQVDFVI-ISVELALDNSLASCYVTYTLYNDGEMKIEQSLAPSETMP 880
            A+    +  ++   + D  I ++ + AL +  A   V YT+   G +K++ +L P + +P
Sbjct: 864  AT--PKLSDMSSSKEEDGSIEVTSKYALIDGKAEATVVYTVLAGGVVKVDYTLIPLDDLP 921

Query: 881  EIPEIGMLFTMNAAFDSLTWYGRGPHENYWDRKTGAKLALHKGSVKEQVTPYLRPQECGN 940
             +P++GM   +   +D + WYG+GP ENY D+  G    +++  + + + PY+ PQE GN
Sbjct: 922  NLPKVGMHLGIRREYDQIRWYGKGPVENYIDKNHGFMAGIYQQPIDQFMEPYVMPQENGN 981

Query: 941  KTDVRWATITNDQG-RGFLIKGLPTVELNALPYSPFELEAYDHFYKLPASDSVTVRVNYK 999
            +TDVRW  +T+  G  G  I     + ++A P++   + A +H Y+L  +  +TV ++  
Sbjct: 982  RTDVRWMELTDKSGENGLNITADSLLSMSAWPFTAENINAAEHTYELDDAGFITVNIDLA 1041

Query: 1000 QMGVGGDDSWQAKTHP 1015
            QMGVGG+DSW     P
Sbjct: 1042 QMGVGGNDSWSDVAQP 1057


Lambda     K      H
   0.316    0.133    0.412 

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: 3437
Number of extensions: 210
Number of successful extensions: 13
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 1034
Length of database: 1080
Length adjustment: 45
Effective length of query: 989
Effective length of database: 1035
Effective search space:  1023615
Effective search space used:  1023615
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: 58 (26.9 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