GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Synechococcus elongatus PCC 7942

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate Synpcc7942_0947 Synpcc7942_0947 ATPase

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



>FitnessBrowser__SynE:Synpcc7942_0947
          Length = 355

 Score =  253 bits (647), Expect = 4e-72
 Identities = 141/339 (41%), Positives = 203/339 (59%), Gaps = 25/339 (7%)

Query: 3   ALQLTNVCKSFGPVEV-LKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEIS 61
           AL+L  + K++ P  V + +++L ++ GEF+  +GPSGCGKST LR+I+GL+  T+G I 
Sbjct: 5   ALELRQLRKAYSPSVVPVANLSLQLQPGEFLTLLGPSGCGKSTTLRLIAGLDQPTSGSIW 64

Query: 62  IGGQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRML 121
           +G + +TT PP  R +AMVFQSYALYPHL+VR+N+ L L+  R    EI  R+ + +  L
Sbjct: 65  LGDREITTLPPGDRDMAMVFQSYALYPHLNVRQNLTLGLQIRRTSAAEIEQRLQQVAHNL 124

Query: 122 SLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLHR 181
            L+  LDRRP++LSGGQRQRVA+GRA+VR+P +FL DEPLSNLDA LR   R ++  L  
Sbjct: 125 ELDHLLDRRPAQLSGGQRQRVALGRALVRQPSVFLLDEPLSNLDALLREQVRAQMKALFS 184

Query: 182 QLSASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIGAPAMNF 241
           Q ++ ++YVTHDQ EA++L+ +I +L  G ++Q+ +P  +Y  PAN FVA FIG+P MN 
Sbjct: 185 QQASPVVYVTHDQTEALSLSHRIAILNGGHLQQLDSPDRIYQAPANAFVAGFIGSPRMNL 244

Query: 242 VP-----------------AQRLGGNPGQFIGIRPEYARISPVGPLAGEVIHV-----EK 279
           +P                    L        G+RPE+ +++   P     I V     E 
Sbjct: 245 LPLPIHSGQAWLGSRALPIPSHLAARSQVLWGLRPEHLKLAT--PEVERAIPVQLHLTEN 302

Query: 280 LGGDTNILVDMGEDLTFTARLFGQHDTNVGETLQFDFDP 318
           LG    + V +  +     RL    D  +   LQ  F+P
Sbjct: 303 LGMQRLLTVAIAANPEVRLRLLMPSDQPIPTDLQVTFEP 341


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: 293
Number of extensions: 9
Number of successful extensions: 1
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: 355
Length adjustment: 29
Effective length of query: 302
Effective length of database: 326
Effective search space:    98452
Effective search space used:    98452
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 Sep 17 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