Alignments for a candidate for lacL in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for lacL in Echinicola vietnamensis KMM 6221, DSM 17526

Align LVIS_2259 + LVIS_2258 (EC 3.2.1.23) (characterized)
to candidate Echvi_0485 Echvi_0485 Beta-galactosidase/beta-glucuronidase

Query= CAZy::ABJ65308.1
         (628 letters)



>FitnessBrowser__Cola:Echvi_0485
          Length = 1038

 Score =  365 bits (936), Expect = e-105
 Identities = 219/628 (34%), Positives = 326/628 (51%), Gaps = 34/628 (5%)

Query: 9   DDPQTFRINQLPAHSDHRGYASVEEATAQHSSLVQS---LDGTWQFAFAPDPVHRFEGFY 65
           +DP     N+  A +    Y S E+A   + +  +S   LDG W+F+    P  R   F+
Sbjct: 29  EDPTAVDRNKEAARAYFITYPSEEKALLGNRTTNESFKTLDGLWKFSLVKRPQDRPTDFF 88

Query: 66  QPDYDRSAFDRLTVPGHIELAGYGQIQYINTAYPWEGHHYRRPAYSMGADQPEKGMFSTD 125
           +P +    +D +TVP + EL GY    Y N AYP+             AD P       +
Sbjct: 89  EPTFKDEDWDDITVPSNWELEGYDMPVYTNVAYPFP------------ADPP----LVDN 132

Query: 126 PQNTVGAYVKHFTLNPALANQRVSIEFDGVEQAMFLWLNGQFVGYAEDSFSRSEFDLTPY 185
             N VG Y + F++     NQ V + F  +     +++NG+ VG  + + + +EF +T Y
Sbjct: 133 QYNPVGTYRRTFSIPSQWDNQEVILHFGSISGYATVYVNGEEVGMTKAAKTPAEFVITDY 192

Query: 186 LQAGQNLLAVEVFKHSTAAFLEDQDMFRFSGIFRSVRLVAKPELHVEDLTIRAGLDDAFQ 245
           L+ G+N LAV+VF+    ++LEDQD +R SGI RSV L A P+L + D  +++GLDD ++
Sbjct: 193 LKTGENTLAVQVFRWHDGSYLEDQDFWRLSGIERSVFLQAVPKLTIWDFFVKSGLDDRYK 252

Query: 246 TGDLKVRLQLTA---ASQLSGTATAQLLTADGQEVWATEQPAAS---TLDLAAAIDHVHL 299
            G L+  +QL A   +    G  + +L   DG++V++  +  ++    +  +  I +V+ 
Sbjct: 253 NGVLEAAIQLRAFEGSDVQGGELSFELQDEDGKQVYSDTKAVSNGDQEVKFSKTIGNVNK 312

Query: 300 WDHHDPYLYQLRITLKDVAGQVVEVVPYPVGFRRIELKDKVMCLNGQRLILNGVNRHEWD 359
           W   +PYLYQ  I+LKD  G+ +  V    GFR++E+KD  + +NGQ +++ GVNRHE  
Sbjct: 313 WSAEEPYLYQYTISLKDSRGRTLAAVSKKTGFRKVEIKDAQLMVNGQSVLVKGVNRHEHH 372

Query: 360 AHRGRAVTMADMTQDLQTFHDNHINAVRTCHYPDQDAWYYLCDQQGIYMMAENNLETHGT 419
             +G       M +D+Q    N+INAVR  HYP    WY LCD+ G+Y++ E N+ETHG 
Sbjct: 373 GVKGHVPDEEIMLRDIQLMKQNNINAVRMSHYPHSPRWYELCDEYGLYVVDEANIETHGM 432

Query: 420 WQKMGAVEPSYNVPGSLPQWQLAVLDRAKSNYEMFKNHPAVLFWSLGNESYAGDNIAAMD 479
             +          P  L  W  A LDR     E  KNHP+++ WS+GNE   G       
Sbjct: 433 GAEWQGRFKKDRHPAYLEAWAPAHLDRIHRLVERDKNHPSIIIWSMGNECGNGPVFYEAY 492

Query: 480 AFYHHADPTRLTHYEGVCRNRVYEDRISDMESMMYDPPRAIEDYL-KNDPQKPFVNCEYM 538
            +    D +RL  +E     +  E+  +D+   MY   R +++Y    D  +PF+ CEY 
Sbjct: 493 NWMKERDDSRLVQFE-----QAGENEDTDIVCPMYPSIRHMQEYADATDKTRPFIMCEYA 547

Query: 539 HDMGNSLGGMASYDALIDQYPMYQGGFIWDFIDQALWVKDEVTGQPVLRYGGDFDDR--H 596
           H MGNS G    Y  +I   P  QGGFIWD++DQ L  KD+  G+    YGGD       
Sbjct: 548 HSMGNSTGNFQEYWDIILDSPHMQGGFIWDWVDQGLLAKDD-NGKEFWAYGGDLGGYFFQ 606

Query: 597 SDYEFSGDGLLFADRTPKPALQEVDYYY 624
           +D  F  +GL+ ADR P PAL EV   Y
Sbjct: 607 NDENFCANGLVTADRKPHPALHEVKKVY 634


Lambda     K      H
   0.320    0.136    0.428 

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: 2021
Number of extensions: 123
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: 628
Length of database: 1038
Length adjustment: 41
Effective length of query: 587
Effective length of database: 997
Effective search space:   585239
Effective search space used:   585239
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 (21.8 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)
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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