GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03040 in Flavobacterium sp. LM5

Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate WP_024981057.1 BXU11_RS07070 ABC transporter ATP-binding protein

Query= reanno::pseudo1_N1B4:Pf1N1B4_3435
         (254 letters)



>NCBI__GCF_002017945.1:WP_024981057.1
          Length = 220

 Score =  137 bits (345), Expect = 2e-37
 Identities = 81/218 (37%), Positives = 125/218 (57%), Gaps = 10/218 (4%)

Query: 7   QDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLNNEE 66
           +++HK Y   EVLKGV L    G+++SI+G+SG+GK+T L+ +  L++P       +NE 
Sbjct: 5   KNIHKFYDQLEVLKGVDLHITKGEIVSIVGASGAGKTTLLQILGTLDRP------TSNEN 58

Query: 67  LKLVANKDGALKAADPKQLQRMRS-RLSMVFQHFNLWSHMTAMENIMEAPVHVLGMSKTE 125
             L+ N +  LK  D K L R R+  L  +FQ   L    TA+EN+   P  + G +K E
Sbjct: 59  SSLLINGEDVLKMND-KALSRFRNLNLGFIFQFHQLLPEFTALENVC-IPAFIAGKNKLE 116

Query: 126 AREKAEHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPELV 185
              +A+  L+ +G++HR    P  +SGGEQQRVA+ARAL  +P+++  DEP+  LD    
Sbjct: 117 TEIEAKKLLDYLGLSHRHHHKPNELSGGEQQRVAVARALINKPDILFADEPSGNLDTTSA 176

Query: 186 GDVLKVMQALAQE-GRTMVVVTHEMGFAREVSNQLVFL 222
            ++ ++   L  E G+T V+VTH    A     +LV +
Sbjct: 177 ENLHQLFFKLRDELGQTFVIVTHNEELANMADRKLVMV 214


Lambda     K      H
   0.317    0.131    0.366 

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: 137
Number of extensions: 7
Number of successful extensions: 4
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: 254
Length of database: 220
Length adjustment: 23
Effective length of query: 231
Effective length of database: 197
Effective search space:    45507
Effective search space used:    45507
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 (21.7 bits)
S2: 46 (22.3 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