GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Phaeacidiphilus oryzae TH49

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate WP_037572389.1 BS73_RS14235 ABC transporter ATP-binding protein

Query= reanno::Phaeo:GFF2754
         (331 letters)



>NCBI__GCF_000744815.1:WP_037572389.1
          Length = 386

 Score =  223 bits (567), Expect = 8e-63
 Identities = 129/354 (36%), Positives = 191/354 (53%), Gaps = 34/354 (9%)

Query: 4   LQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEISIG 63
           L+LT + K FG    +  ++LT+  G F   +G SGCGK+T LR+ISGLE  TAG I +G
Sbjct: 19  LRLTGLTKKFGSFTAVDGVDLTIAQGSFFALLGASGCGKTTTLRMISGLEAPTAGRIHLG 78

Query: 64  GQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRMLSL 123
            Q VT   P +R +  VFQ+YAL+PHL + EN+A  L+  R+    +   V +   ++ L
Sbjct: 79  DQDVTDRKPYRRPVNTVFQNYALFPHLDIFENVAFGLR--RRGIRSVKKPVEDMLDLVEL 136

Query: 124 EDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLHRQL 183
                R+P++LSGGQ+QR+A+ RA++ +P++ L DEPL  LD  LR   ++E+ R+  ++
Sbjct: 137 GHLARRKPTQLSGGQQQRIALARALINQPQVLLLDEPLGALDLKLRRQMQIELKRIQLEV 196

Query: 184 SASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIGAPAMNFVP 243
             + ++VTHDQ EAMT+AD I V+  GRIEQ+G+P ELY NP   FVA F+G   +    
Sbjct: 197 GLTFVHVTHDQEEAMTMADTIAVMNHGRIEQLGSPAELYENPNTTFVANFLGQSNLIAGT 256

Query: 244 AQRLGGNPGQ----------------------FIGIRPEYARI--------SPVGPLAGE 273
            + + G+  Q                       +G+RPE  RI        S    L G+
Sbjct: 257 VESVSGDVVQVAAHGRSLALPAARCRTTSGPVILGVRPEKVRIAKTEAEVPSGANHLTGK 316

Query: 274 VIHVEKLGGDTNILVDM--GEDLTFTARLFGQHDTNVGETLQFDFDPANCLSFD 325
           V     +G  T  LV++  GE+L    +  GQ     G  +   +DP+     D
Sbjct: 317 VTDASFIGVSTQYLVELPSGEELAVFEQNTGQEIQRPGAEVVVHWDPSQGFGLD 370


Lambda     K      H
   0.320    0.137    0.391 

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: 317
Number of extensions: 24
Number of successful extensions: 2
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: 331
Length of database: 386
Length adjustment: 29
Effective length of query: 302
Effective length of database: 357
Effective search space:   107814
Effective search space used:   107814
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: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. 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