GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK in Herbaspirillum seropedicae SmR1

Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate HSERO_RS16715 HSERO_RS16715 sugar ABC transporter ATP-binding protein

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



>FitnessBrowser__HerbieS:HSERO_RS16715
          Length = 361

 Score =  338 bits (866), Expect = 2e-97
 Identities = 187/358 (52%), Positives = 239/358 (66%), Gaps = 11/358 (3%)

Query: 1   MTGLLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDM 60
           M  + ++ ++K +G+  +I G+D+DI +GEF V VGPSGCGKSTLLRM+AGLEEITGG++
Sbjct: 1   MASVQIRAVKKQFGSTQIIRGVDIDIADGEFTVLVGPSGCGKSTLLRMLAGLEEITGGEI 60

Query: 61  FIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADM 120
            I G  VN+V P  R IAMVFQ+YALYPHMTV DNMAF + +A++ K  +D RV+ AAD+
Sbjct: 61  LIGGTVVNNVQPKDRDIAMVFQNYALYPHMTVRDNMAFSLTLAKKDKAFVDERVKKAADI 120

Query: 121 LQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLS 180
           L L   LDR P+ LSGGQRQRVA+GRAI R+P+VFLFDEPLSNLDA LRV  R EI +L 
Sbjct: 121 LGLNQLLDRYPRQLSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRTEIKELH 180

Query: 181 ERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAM 240
           +R+  TT IYVTHDQ+EAMT+AD+IVV+  G +EQ G PL+LY+ PANLFVA FIGSPAM
Sbjct: 181 QRLK-TTSIYVTHDQIEAMTMADQIVVMRDGLVEQRGRPLDLYDYPANLFVAGFIGSPAM 239

Query: 241 NVIPATITATGQQTAVSLAGGKSVTLDVPTNAS---ENGKTASFGVRPEDLRVTEADDFL 297
           N IPAT+        V  A G  V    P  A+    +G+  ++GVRPE L +  A   +
Sbjct: 240 NFIPATLRRNATGAEVEFADGTRV--PAPYGAALQGNDGQKVTYGVRPEHLSIGAAGQGI 297

Query: 298 FEGTVSIVEALGEVTLLYIE-GLVENEPIIAKMPGIARVGRGDKVRFTADKAKLHLFD 354
               V +VE  G  T ++   G      I  +       G GD +    D ++ HLFD
Sbjct: 298 -ATKVIVVEPTGADTEVFSRFGDTSLTSIFRERHDF---GAGDVIHLVPDHSRTHLFD 351


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: 386
Number of extensions: 21
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: 362
Length of database: 361
Length adjustment: 29
Effective length of query: 333
Effective length of database: 332
Effective search space:   110556
Effective search space used:   110556
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.

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