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 (Gal4214-1) (EC 3.2.1.23) (characterized)
to candidate Echvi_0485 Echvi_0485 Beta-galactosidase/beta-glucuronidase

Query= CAZy::AAX48919.1
         (1046 letters)



>FitnessBrowser__Cola:Echvi_0485
          Length = 1038

 Score = 1048 bits (2709), Expect = 0.0
 Identities = 515/1049 (49%), Positives = 690/1049 (65%), Gaps = 15/1049 (1%)

Query: 1    MNMKKRTILTSIFAFISIIVFAQEKPSRNDWENPEVFQINREPARAAFLPFADEASAIAD 60
            M  KK  +  ++ A +  ++ AQ   S+N+WE+P     N+E ARA F+ +  E  A+  
Sbjct: 1    MQFKKLWMTGALVAALGGLLHAQ---SQNEWEDPTAVDRNKEAARAYFITYPSEEKALLG 57

Query: 61   DYTRSPWYMSLDGKWKFNWSPTPDERPKDFFNTDFNTTTWKEIGVPSNWELVGYGIPIYT 120
            + T +  + +LDG WKF+    P +RP DFF   F    W +I VPSNWEL GY +P+YT
Sbjct: 58   NRTTNESFKTLDGLWKFSLVKRPQDRPTDFFEPTFKDEDWDDITVPSNWELEGYDMPVYT 117

Query: 121  NITYPFVKNPPFIDHADNPVGSYRRTFELPENWDGRRVYLHFEGGTSAMYVWINGEKVGY 180
            N+ YPF  +PP +D+  NPVG+YRRTF +P  WD + V LHF   +    V++NGE+VG 
Sbjct: 118  NVAYPFPADPPLVDNQYNPVGTYRRTFSIPSQWDNQEVILHFGSISGYATVYVNGEEVGM 177

Query: 181  SQNTKSPTEFDITKYVKVGKNQVAVEVYRWSDGSYLEDQDFWRLSGIDRSVYLYSTANTR 240
            ++  K+P EF IT Y+K G+N +AV+V+RW DGSYLEDQDFWRLSGI+RSV+L +     
Sbjct: 178  TKAAKTPAEFVITDYLKTGENTLAVQVFRWHDGSYLEDQDFWRLSGIERSVFLQAVPKLT 237

Query: 241  IADFFARPDLDTSYKNGSLSVDIKLKNANSVAKNNQTVEAKLVDAAGKEVFIKTIKINLG 300
            I DFF +  LD  YKNG L   I+L+           +  +L D  GK+V+  T  ++ G
Sbjct: 238  IWDFFVKSGLDDRYKNGVLEAAIQLRAFEGSDVQGGELSFELQDEDGKQVYSDTKAVSNG 297

Query: 301  ANTVSSTTFEQMVKSPKLWNNETPNLYTLVLTLKDENGKFVETVATSIGFRKVELKNGQL 360
               V    F + + +   W+ E P LY   ++LKD  G+ +  V+   GFRKVE+K+ QL
Sbjct: 298  DQEVK---FSKTIGNVNKWSAEEPYLYQYTISLKDSRGRTLAAVSKKTGFRKVEIKDAQL 354

Query: 361  LVNGIRIMVHGVNIHEHNPKTGHYQDEATMMKDIKLMKQLNINAVRCSHYPNNLLWVKLC 420
            +VNG  ++V GVN HEH+   GH  DE  M++DI+LMKQ NINAVR SHYP++  W +LC
Sbjct: 355  MVNGQSVLVKGVNRHEHHGVKGHVPDEEIMLRDIQLMKQNNINAVRMSHYPHSPRWYELC 414

Query: 421  NKYGLFLVDEANIETHGMGAELQGSFDKTKHPAYLPEWKAAHMDRIYSLVERDKNQPSII 480
            ++YGL++VDEANIETHGMGAE QG F K +HPAYL  W  AH+DRI+ LVERDKN PSII
Sbjct: 415  DEYGLYVVDEANIETHGMGAEWQGRFKKDRHPAYLEAWAPAHLDRIHRLVERDKNHPSII 474

Query: 481  LWSLGNECGNGPVFHEAYNWIKNRDKTRLVQFEQAGEQENTDVVCPMYPSMEYMKEYANR 540
            +WS+GNECGNGPVF+EAYNW+K RD +RLVQFEQAGE E+TD+VCPMYPS+ +M+EYA+ 
Sbjct: 475  IWSMGNECGNGPVFYEAYNWMKERDDSRLVQFEQAGENEDTDIVCPMYPSIRHMQEYADA 534

Query: 541  KDVKRPFIMCEYSHAMGNSNGNFQEYWDIIHSSTNMQGGFIWDWVDQGFEETDEAGRKYW 600
             D  RPFIMCEY+H+MGNS GNFQEYWDII  S +MQGGFIWDWVDQG    D+ G+++W
Sbjct: 535  TDKTRPFIMCEYAHSMGNSTGNFQEYWDIILDSPHMQGGFIWDWVDQGLLAKDDNGKEFW 594

Query: 601  AYGGDMGGQNYTNDQNFCHNGLVWPDRTPHPGAFEVKKVYQDILFKGVNLDKGIIEVENG 660
            AYGGD+GG  + ND+NFC NGLV  DR PHP   EVKKVYQDILF   + +KG + V+N 
Sbjct: 595  AYGGDLGGYFFQNDENFCANGLVTADRKPHPALHEVKKVYQDILF-DYSPEKG-LHVQNL 652

Query: 661  FGYTNLDKYLFKFEVLKNGLVIKSGVINIRLAPQSKKQIQIELPKLTTEDGVEYLLNVFA 720
            F +TNLD+Y FK+E ++ G V+K+G  ++ L+   +K +Q+ LP +      E  LNV+A
Sbjct: 653  FDFTNLDQYAFKWEWVEEGEVVKTGDFDVDLSADEEKYVQLNLPSV---GDAETFLNVYA 709

Query: 721  YTKEGTELLPQNFEIAREQFSIGESNYFVKVAKASTNPIVKDSQDAITLSANGVEVTINK 780
            YTK    L+P   E+AREQF++ E  YF  +   + N  V+ ++D +T + + V    + 
Sbjct: 710  YTKNTEALVPAGHEVAREQFALNEGYYFDHLEAVTGNLQVEQTEDLLTFATDKVTGAFDL 769

Query: 781  KTGLMQKYT--SGEENYFNQMPVPNFWRAPTDNDFGNYMQVNSNVWRTVGRFSSLDSIEV 838
            K G  +KYT   GE      +P P FWRAP DNDFGN+M     VWR+      +  ++V
Sbjct: 770  KRGNFRKYTLKDGEPWMVRSLPSPYFWRAPIDNDFGNHMPSRLGVWRSAHLGQKVLDVQV 829

Query: 839  KEVSTQ-TTVVAHLFLKDIASTYTITYSMDADGSLTLQNSFKAGEMALSEMPRFGMLFSL 897
             E S +   +  +  L +I   YT+TY + +DG++ +  +       L E+PR+GM   L
Sbjct: 830  GEKSDEGIQITVNYELTNINVPYTVTYQIQSDGAVKVTAAMDLEGRDLPELPRYGMRMEL 889

Query: 898  KKELDNFSYYGRGPWENYQDRNTSSLKGIYESKVADQ-YVPYTRPQENGYKTDIRWITLT 956
              +  N +YYGRGPWENY DR  SS  G Y  +V +Q Y  Y RPQE+G KTD+RW+TL 
Sbjct: 890  PGQYGNLAYYGRGPWENYSDRKHSSFIGQYNDQVENQFYWDYVRPQESGNKTDVRWLTLR 949

Query: 957  NSSGNGIEILGLQPLGVSALNNYPEDFDPGLTKKQQHTNDITPRDEVIICVDLAQRGLGG 1016
            N  G GI+I G+QPL  SAL+   ED DPGLTKKQQH  DI P++ V + +D  QRGLGG
Sbjct: 950  NDKGQGIQIQGIQPLSFSALDVSVEDLDPGLTKKQQHPTDIKPKNTVYLHIDWKQRGLGG 1009

Query: 1017 DNSWGAMPHEQYQLRNKAYSYGFVIKPIK 1045
            D SWGA PH+ Y+L +  Y Y +VI+ ++
Sbjct: 1010 DTSWGAYPHKPYRLEDDHYEYSYVIRLVE 1038


Lambda     K      H
   0.316    0.134    0.410 

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: 3375
Number of extensions: 184
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: 1046
Length of database: 1038
Length adjustment: 45
Effective length of query: 1001
Effective length of database: 993
Effective search space:   993993
Effective search space used:   993993
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