GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Azospirillum brasilense Sp245

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate AZOBR_RS27980 AZOBR_RS27980 sugar ABC transporter ATP-binding protein

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



>FitnessBrowser__azobra:AZOBR_RS27980
          Length = 360

 Score =  315 bits (808), Expect = 8e-91
 Identities = 166/310 (53%), Positives = 214/310 (69%), Gaps = 23/310 (7%)

Query: 1   MTALQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEI 60
           M ++ + ++ KS+G   VL  +++ + DGEFV  VGPSGCGKSTLLR+I+GLE+A  GEI
Sbjct: 1   MASVIIRDLRKSYGGTPVLHGVSVDIADGEFVALVGPSGCGKSTLLRMIAGLEEAGEGEI 60

Query: 61  SIGGQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRM 120
            IGG+ V   PP  R IAMVFQ+YALYPH++V +N+  AL  +   + EIAARVA A+ +
Sbjct: 61  RIGGRLVNDVPPKDRDIAMVFQNYALYPHMTVAQNLGFALTLKDVDRGEIAARVARAAEV 120

Query: 121 LSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLH 180
           L L   LDRRP +LSGGQRQRVA+GRA+VR+P+LFLFDEPLSNLDA LR+  R EI  LH
Sbjct: 121 LGLSALLDRRPGQLSGGQRQRVAMGRAIVRDPRLFLFDEPLSNLDAKLRVQMRAEIKALH 180

Query: 181 RQLSASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIGAPAMN 240
           ++L  S IYVTHDQIEAMT+AD+IVV+RDGR+EQ G P++LY+ PANRFVA FIG+PAMN
Sbjct: 181 QRLRTSAIYVTHDQIEAMTMADRIVVMRDGRVEQAGAPLDLYDRPANRFVAGFIGSPAMN 240

Query: 241 FVPAQ---------RLGGNPG--------------QFIGIRPEYARISPVGPLAGEVIHV 277
           F+  +         RL G P                 +G+RPE+A I P   +   V  V
Sbjct: 241 FLTGRIAVNGRASFRLDGGPDLPLSAVPLEADGRPAVLGLRPEHALIDPEEGVPLHVAVV 300

Query: 278 EKLGGDTNIL 287
           E  G +T ++
Sbjct: 301 EPTGSETQVV 310


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: 386
Number of extensions: 20
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: 360
Length adjustment: 29
Effective length of query: 302
Effective length of database: 331
Effective search space:    99962
Effective search space used:    99962
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