GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Herbaspirillum seropedicae SmR1

Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate HSERO_RS01355 HSERO_RS01355 sugar ABC transporter ATP-binding protein

Query= reanno::BFirm:BPHYT_RS16095
         (369 letters)



>FitnessBrowser__HerbieS:HSERO_RS01355
          Length = 381

 Score =  375 bits (963), Expect = e-108
 Identities = 202/375 (53%), Positives = 260/375 (69%), Gaps = 11/375 (2%)

Query: 1   MASVTLRNIRKAY-DENEVMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGGD 59
           MAS+TLR  +KAY D   V+R+++LDI + EF VF+GPSGCGKSTL+R IAGLED++ GD
Sbjct: 1   MASITLRAAQKAYGDAPPVIRNVDLDIGEHEFCVFLGPSGCGKSTLLRSIAGLEDLTSGD 60

Query: 60  LTIDGMRVNDVAPAKRGIAMVFQSYALYPHMTLYDNMAFGLKLAGTKKPEIDAAVRNAAK 119
           L I G RVNDV  A+R +AMVFQSYAL+PHMT+Y+NM+FGL LA   K EI+  VR AA+
Sbjct: 61  LFIGGKRVNDVPSAQRSVAMVFQSYALFPHMTVYENMSFGLTLAKLPKAEIEQKVREAAR 120

Query: 120 ILHIDHLLDRKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFARL 179
           IL ++ LL RKPK+LSGGQRQRVAIGRAI R+P VFLFDEPLSNLDA LR + R+E ARL
Sbjct: 121 ILQLEELLQRKPKELSGGQRQRVAIGRAIVRRPGVFLFDEPLSNLDATLRSQTRIEIARL 180

Query: 180 HDEL-KTTMIYVTHDQVEAMTLADKIVVLSA-------GNLEQVGSPTMLYHAPANRFVA 231
           H +  + +++YVTHDQVEAMTLAD+IV+L A       G++ QVG+P  LYH P NRFVA
Sbjct: 181 HRQFEQASVVYVTHDQVEAMTLADRIVLLHAGADTQRFGSIAQVGTPMELYHHPRNRFVA 240

Query: 232 GFIGSPKMNFMEGVVQSVTHDGVTVRYETGETQRVAVEPAAVKQGDKVTVGIRPEHLHVG 291
           GFIGSP+MNF+   V  V  +G+ VR    E   +     A++ G  VTVG+RPEH+ +G
Sbjct: 241 GFIGSPRMNFLPAQVAGVQENGILVRLSGSEETLLVAAQGALQPGQMVTVGVRPEHMEIG 300

Query: 292 -MAEDGISARTMAVESLGDAAYLYAESSVAPDGLIARIPPLERHTKGETQKLGATPEHCH 350
              + GI    + VE LG+  Y++ +   A   L+A+     R T+GE  ++   P   +
Sbjct: 301 SQGQYGIHREVVLVERLGEQTYVHLDEP-AGQPLVAKAAGDARITRGERVRVAIAPACAY 359

Query: 351 LFDSAGKAFQRKIVE 365
           LFD  G A  R  V+
Sbjct: 360 LFDQDGLALTRTQVQ 374


Lambda     K      H
   0.320    0.135    0.384 

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: 415
Number of extensions: 17
Number of successful extensions: 5
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: 369
Length of database: 381
Length adjustment: 30
Effective length of query: 339
Effective length of database: 351
Effective search space:   118989
Effective search space used:   118989
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: 50 (23.9 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