GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK in Pantoea rwandensis LMG 26275

Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate WP_084934899.1 HA51_RS12950 ABC transporter ATP-binding protein

Query= reanno::Smeli:SMc03065
         (362 letters)



>NCBI__GCF_002095475.1:WP_084934899.1
          Length = 367

 Score =  270 bits (691), Expect = 3e-77
 Identities = 150/355 (42%), Positives = 214/355 (60%), Gaps = 10/355 (2%)

Query: 1   MTGLLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDM 60
           M+ L L  I K++G    ++ I  D  EG FV  +GPSGCGKSTLLR IAGLE    G++
Sbjct: 1   MSHLSLHHITKAWGEKIALNDISFDAAEGSFVALLGPSGCGKSTLLRTIAGLETADSGEI 60

Query: 61  FIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADM 120
                 +  +PPS+R ++MVFQSYAL+PH+ V +N+ FG++   E K+    R+   + +
Sbjct: 61  HFKHSDITHLPPSQRKLSMVFQSYALFPHLNVRENLLFGLKARGEDKQTFTTRLDDVSKL 120

Query: 121 LQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLS 180
           ++L   LDRLP  LSGGQ+QRVA+GRA+  N  + L DEPLSNLDA LR + R EI  L 
Sbjct: 121 MELDKLLDRLPSQLSGGQQQRVALGRAVIANNNLCLMDEPLSNLDAKLRQSMRREIRALQ 180

Query: 181 ERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAM 240
           ++++  TM+YVTHDQ EAM++AD I++L+ GHIEQ G P +LY  PA +F A+FIG+P M
Sbjct: 181 KKLA-LTMLYVTHDQTEAMSMADSIILLNDGHIEQHGTPNDLYNNPATIFAAQFIGAPPM 239

Query: 241 NVIPATITATGQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVTEADDFLFEG 300
           N++P  + A G+Q  +S        L  P     +    S G+R ED+++  AD+     
Sbjct: 240 NILP--LHAKGEQHYLS-------HLQTPVVERCDEVALSLGLRAEDIQLISADNAALTA 290

Query: 301 TVSIVEALGEVTLLYIEGLVENEPIIAKMPGIARVGRGDKVRFTADKAKLHLFDT 355
            V   E +G  TLL  +    +E +  K+PG+ R   G  V      A+ +LF +
Sbjct: 291 RVISYEYMGSDTLLACQLAGLSELVTVKVPGMQRYDEGSLVGLQWSAARQYLFSS 345


Lambda     K      H
   0.320    0.137    0.387 

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: 295
Number of extensions: 10
Number of successful extensions: 3
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: 362
Length of database: 367
Length adjustment: 29
Effective length of query: 333
Effective length of database: 338
Effective search space:   112554
Effective search space used:   112554
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 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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