GapMind for catabolism of small carbon sources

 

Aligments for a candidate for natE in Herbaspirillum seropedicae SmR1

Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate HSERO_RS23270 HSERO_RS23270 ABC transporter

Query= TCDB::P73650
         (240 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS23270 HSERO_RS23270 ABC
           transporter
          Length = 234

 Score =  196 bits (497), Expect = 4e-55
 Identities = 107/232 (46%), Positives = 150/232 (64%), Gaps = 4/232 (1%)

Query: 4   LLVVKDVFAGYVADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEII 63
           +L V+DV  GY     ILQG++  +  GE+VT++G NGAGK+T  K+I G++ P QG ++
Sbjct: 2   ILQVEDVH-GYYGKSHILQGVSLQVDAGEVVTLLGRNGAGKTTTLKSIVGVVPPVQGRVL 60

Query: 64  FKGENITGLGSDQIVRRGMCYVPQVCNVFGSLTVAENLDMGAFLHQGPTQTLKDRIYTMF 123
           F+G+ I+GL S +I  RG+C VP+   +F  LTV ENL M A   +  +    + IY +F
Sbjct: 61  FEGQLISGLPSYKIAARGVCLVPEHRGIFKLLTVEENLTMAA---RKESAWGLEEIYAIF 117

Query: 124 PKLAQRRNQRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIKAIN 183
           P+L +RR    G LSGGE+QMLA+ RALM  P +L+LDEP   L+P++V ++ AQI+ I 
Sbjct: 118 PRLKERRKNGGGQLSGGEQQMLAIARALMTHPRVLMLDEPVEGLAPVIVDEIVAQIRQIK 177

Query: 184 ATGKAIILVEQNAKQALMMADRGYVLENGRDKLEGSGQSLLNDPLVGELYLG 235
           ATG +IILVEQN +    +ADR Y++E GR    GS    L D  V + YLG
Sbjct: 178 ATGMSIILVEQNLEVCTQLADRHYIVEQGRIVYHGSNAEFLADEGVKDRYLG 229


Lambda     K      H
   0.320    0.139    0.393 

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: 174
Number of extensions: 6
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: 240
Length of database: 234
Length adjustment: 23
Effective length of query: 217
Effective length of database: 211
Effective search space:    45787
Effective search space used:    45787
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: 46 (22.3 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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