GapMind for catabolism of small carbon sources

 

Alignments for a candidate for uxuL in Amantichitinum ursilacus IGB-41

Align Senescence marker protein-30 family protein (characterized, see rationale)
to candidate WP_053939460.1 WG78_RS19225 SMP-30/gluconolactonase/LRE family protein

Query= uniprot:Q888H2
         (294 letters)



>NCBI__GCF_001294205.1:WP_053939460.1
          Length = 301

 Score =  144 bits (362), Expect = 3e-39
 Identities = 97/273 (35%), Positives = 133/273 (48%), Gaps = 10/273 (3%)

Query: 26  LYWVDIPNGELHRWDSSQDRTRSWKAPQMLACIAADSRGGWIAGMENGLYHLQPCDDGSL 85
           L+W +I   EL + D    + R W  PQ + C A       +    +    L     G++
Sbjct: 33  LWWTNIHAKELWQLDLRTGQHRYWSTPQRVCCFAFTQDDDVLLVAFDAGLALFNTASGAI 92

Query: 86  ISTLLASVEHAQTGMRFNDGRCDRQGRFWAGTMLMDMAAGAVVGALYRYSAGQKTLEAQL 145
               L  VE    G R NDGR DR G    GTM    A     G  YR+    +  +  L
Sbjct: 93  --KRLTPVEPETPGTRCNDGRVDRAGNLVFGTMHERSAEAK--GHFYRFDTESRLQQLAL 148

Query: 146 KDLIVPNGLAFSPDGKTMYLSDSHPAVQKIWAFDYDTDSGTPHDRRLFVDMNNYLGRPDG 205
             + + N LAFSPDG T+Y  DS     KI    YD+ +G   +  +F D+ + +  PDG
Sbjct: 149 PAIAISNSLAFSPDGGTLYWCDS--LQHKIMQCAYDSVTGAIAEISVFHDLGDTVIEPDG 206

Query: 206 AAIDADGCYWICGNDAGLVHRFTPNGKLDRSLVVPVKKPAMCAFGGPNLDTLFVTSIRPG 265
           + +DA G  W        V R+ P+G +DR + +PV +P    FGGP  +TLF+TS R G
Sbjct: 207 STVDAAGYLWNAEWAGHCVTRYAPDGSIDRKIHLPVAQPTCVTFGGPEQNTLFITSARAG 266

Query: 266 GD---LSDQPLAGGVFALR-PGVKGLEEPVFQG 294
            D   L+ QP AG VFAL  PGV+GL E ++ G
Sbjct: 267 LDDAALAQQPEAGSVFALEIPGVRGLPENIWLG 299


Lambda     K      H
   0.320    0.138    0.441 

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: 330
Number of extensions: 26
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: 294
Length of database: 301
Length adjustment: 26
Effective length of query: 268
Effective length of database: 275
Effective search space:    73700
Effective search space used:    73700
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: 48 (23.1 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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:

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:

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:

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:

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