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_RS01355 HSERO_RS01355 sugar ABC transporter ATP-binding protein

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



>FitnessBrowser__HerbieS:HSERO_RS01355
          Length = 381

 Score =  360 bits (923), Expect = e-104
 Identities = 195/366 (53%), Positives = 249/366 (68%), Gaps = 10/366 (2%)

Query: 1   MTGLLLKDIRKSYG-AVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGD 59
           M  + L+  +K+YG A  VI  +DLDI E EF VF+GPSGCGKSTLLR IAGLE++T GD
Sbjct: 1   MASITLRAAQKAYGDAPPVIRNVDLDIGEHEFCVFLGPSGCGKSTLLRSIAGLEDLTSGD 60

Query: 60  MFIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAAD 119
           +FI G+RVNDVP ++R +AMVFQSYAL+PHMTVY+NM+FG+ +A+  K EI+++VR AA 
Sbjct: 61  LFIGGKRVNDVPSAQRSVAMVFQSYALFPHMTVYENMSFGLTLAKLPKAEIEQKVREAAR 120

Query: 120 MLQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKL 179
           +LQL   L R PK LSGGQRQRVAIGRAI R P VFLFDEPLSNLDA LR  TRIEIA+L
Sbjct: 121 ILQLEELLQRKPKELSGGQRQRVAIGRAIVRRPGVFLFDEPLSNLDATLRSQTRIEIARL 180

Query: 180 SERMSDTTMIYVTHDQVEAMTLADRIVVLSA-------GHIEQVGAPLELYERPANLFVA 232
             +    +++YVTHDQVEAMTLADRIV+L A       G I QVG P+ELY  P N FVA
Sbjct: 181 HRQFEQASVVYVTHDQVEAMTLADRIVLLHAGADTQRFGSIAQVGTPMELYHHPRNRFVA 240

Query: 233 RFIGSPAMNVIPATITATGQQ-TAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVT 291
            FIGSP MN +PA +    +    V L+G +   L     A + G+  + GVRPE + + 
Sbjct: 241 GFIGSPRMNFLPAQVAGVQENGILVRLSGSEETLLVAAQGALQPGQMVTVGVRPEHMEIG 300

Query: 292 EADDFLFEGTVSIVEALGEVTLLYIEGLVENEPIIAKMPGIARVGRGDKVRFTADKAKLH 351
               +     V +VE LGE T ++++     +P++AK  G AR+ RG++VR     A  +
Sbjct: 301 SQGQYGIHREVVLVERLGEQTYVHLDE-PAGQPLVAKAAGDARITRGERVRVAIAPACAY 359

Query: 352 LFDTNG 357
           LFD +G
Sbjct: 360 LFDQDG 365


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: 406
Number of extensions: 16
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: 381
Length adjustment: 30
Effective length of query: 332
Effective length of database: 351
Effective search space:   116532
Effective search space used:   116532
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