GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livF in Sinorhizobium meliloti 1021

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate SMc01948 SMc01948 high-affinity branched-chain amino acid ABC transporter ATP-binding protein

Query= uniprot:Q1MCU3
         (247 letters)



>lcl|FitnessBrowser__Smeli:SMc01948 SMc01948 high-affinity
           branched-chain amino acid ABC transporter ATP-binding
           protein
          Length = 241

 Score =  416 bits (1068), Expect = e-121
 Identities = 211/238 (88%), Positives = 224/238 (94%)

Query: 10  PLLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVV 69
           PLL V  VETYYGNIRAL GVD+ V++GEIV+LIGANGAGKSTLMMTICGSPQARTGSV 
Sbjct: 4   PLLHVRSVETYYGNIRALNGVDMEVHRGEIVALIGANGAGKSTLMMTICGSPQARTGSVH 63

Query: 70  FEGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLKHFAEDVEKIFTL 129
           F+G+DITR+PTHEIARLRIAQSPEGRRIFPRMTVLENLQMGA LDNLKHF EDVEK+FTL
Sbjct: 64  FDGQDITRLPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGASLDNLKHFKEDVEKVFTL 123

Query: 130 FPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIRKL 189
           FPRLKER AQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAI+ L
Sbjct: 124 FPRLKERQAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIKVL 183

Query: 190 NEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAYLEGGRH 247
           N+ EGLTVFLVEQNAF AL+LS R YVMVNG+VTMSGSGK+LLANPEVRAAYLEGGRH
Sbjct: 184 NKNEGLTVFLVEQNAFGALKLSDRGYVMVNGRVTMSGSGKDLLANPEVRAAYLEGGRH 241


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: 319
Number of extensions: 3
Number of successful extensions: 1
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: 247
Length of database: 241
Length adjustment: 24
Effective length of query: 223
Effective length of database: 217
Effective search space:    48391
Effective search space used:    48391
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 paper from 2022 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