GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Mesorhizobium ciceri biovar biserrulae WSM1271

Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate WP_013528159.1 MESCI_RS01435 ABC transporter ATP-binding protein

Query= TCDB::Q8DQH8
         (254 letters)



>NCBI__GCF_000185905.1:WP_013528159.1
          Length = 311

 Score =  211 bits (536), Expect = 2e-59
 Identities = 104/250 (41%), Positives = 160/250 (64%)

Query: 2   ALLEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVT 61
           ALL ++ ++  FGG+ A+ D+ L + +GE+  +IGPNGAGK++L N+++GVY P  G V 
Sbjct: 51  ALLSLQGISLSFGGVVALADIDLSVRQGEIRAIIGPNGAGKSSLINVISGVYRPDRGHVQ 110

Query: 62  LDGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRLPAF 121
           LDG         ++A LG+ RTFQN+ LFK L+VLDNV        + +     L +   
Sbjct: 111 LDGTSYAQVPTQRLAHLGVARTFQNLALFKGLSVLDNVASGLAYKVRSNFAGQVLGIGRS 170

Query: 122 YKSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPAAG 181
              +++ +++A ++L+   L    + L   L YG Q+R+E+ RAL  EP++L LDEP AG
Sbjct: 171 RGEQRDSRSRAEQILEFLHLTAIRDRLVGTLPYGLQKRVELARALVAEPRLLLLDEPMAG 230

Query: 182 MNPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEIKT 241
           M   E +E+   +R  +D F  T++LIEHD+ +VM +++RI VL+YGR IA  TPDE++ 
Sbjct: 231 MTASEKSEMASFVRAARDRFATTVVLIEHDVGVVMGLSDRIAVLDYGRKIADATPDEVRN 290

Query: 242 NKRVIEAYLG 251
           ++RVI+AYLG
Sbjct: 291 DQRVIDAYLG 300


Lambda     K      H
   0.319    0.139    0.385 

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: 194
Number of extensions: 7
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: 254
Length of database: 311
Length adjustment: 26
Effective length of query: 228
Effective length of database: 285
Effective search space:    64980
Effective search space used:    64980
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 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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