GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2562 in Mesorhizobium ciceri WSM1271

Align ABC transporter for L-Histidine, periplasmic substrate-binding component 2 (characterized)
to candidate YP_004142525.1 Mesci_3352 family 3 extracellular solute-binding protein

Query= reanno::acidovorax_3H11:Ac3H11_2562
         (321 letters)



>NCBI__GCF_000185905.1:YP_004142525.1
          Length = 316

 Score =  360 bits (925), Expect = e-104
 Identities = 181/310 (58%), Positives = 228/310 (73%), Gaps = 2/310 (0%)

Query: 11  LAAAAACVMALAAPAQAQDTKIVLGMSGWTGFAPLTLADKAGIFKKNGLDVEIKMIPQKD 70
           L A       L+APA A  T + +G+SGWTGFAPLTLA +AGIF+K+GLDV +K +PQ  
Sbjct: 7   LTATLTLAAGLSAPAMAA-TSVTIGISGWTGFAPLTLAKQAGIFEKHGLDVTLKKVPQAS 65

Query: 71  RHLALASKSIQCAATTVETHVAWNANGVPIVQIFQMDKSYGADGIAVRGDIKSFADLKGK 130
           R LA+AS  +QCAATTVET + WNA+GV   QIFQ+DKSYGADGI  R +IK+ ADLKGK
Sbjct: 66  RPLAIASGDLQCAATTVETWLVWNASGVTTKQIFQLDKSYGADGIVARNNIKTVADLKGK 125

Query: 131 TIGVDAPGTAPYFGLAWMLSKNGMSLKDVKTTTLSPQAAAQAFVAGQNDAAMTYEPYLST 190
            +   APGT+PYF LAW+L+KNG+S KDV    L P AAAQAF+AGQNDAA+TYEP++S 
Sbjct: 126 NVASSAPGTSPYFMLAWVLNKNGISTKDVTVVNLEPDAAAQAFLAGQNDAAVTYEPFISA 185

Query: 191 VRDNPAAGKILATTLDYPMVMDTVGCDPTWLKANGKAAQALANSYFQALDMIKADPAKSN 250
           VRD    G ILATTLDYPMV+DTVGC P +LK N  AA+ALA+SYF ALD+IK+DP KS 
Sbjct: 186 VRDKSDQGHILATTLDYPMVLDTVGCTPEFLKTNPDAAKALADSYFDALDLIKSDPQKSY 245

Query: 251 EIMGAAVKQTGEQFAKSSSFLRWQDKAANQKFFAGELTTFMKDATAILLEAGIIRKANED 310
           E MGA VKQ+ ++F  S+ +L+W D+A N++FF  E   F K A  +LL+ G+I++A  D
Sbjct: 246 ETMGADVKQSAKEFEDSAKYLKWADRAENKQFFTKEFQDFSKTAGELLLQMGLIKEA-PD 304

Query: 311 LAVTFDASFI 320
           +    D S +
Sbjct: 305 VTTLADTSAV 314


Lambda     K      H
   0.317    0.129    0.374 

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: 342
Number of extensions: 11
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: 321
Length of database: 316
Length adjustment: 27
Effective length of query: 294
Effective length of database: 289
Effective search space:    84966
Effective search space used:    84966
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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