GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21725 in Rhizorhabdus wittichii RW1

Align ABC transporter for D-Glucosamine, putative ATPase component (characterized)
to candidate WP_011950868.1 SWIT_RS00070 ATP-binding cassette domain-containing protein

Query= reanno::pseudo6_N2E2:Pf6N2E2_2050
         (263 letters)



>NCBI__GCF_000016765.1:WP_011950868.1
          Length = 252

 Score =  139 bits (351), Expect = 4e-38
 Identities = 90/234 (38%), Positives = 132/234 (56%), Gaps = 11/234 (4%)

Query: 16  IRGLRKQYGPLEVLKGVDLSMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQIMLDGE 75
           + G+RK +G   VL GVDL+++RG  + +IG SGSGK+ +L+C+  L     G I +DGE
Sbjct: 9   LEGVRKAFGGNAVLDGVDLAIERGESLVIIGQSGSGKSVMLKCILGLIRPDRGAIRVDGE 68

Query: 76  SIGYDDIDGKRVRHPEKVIARHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKLPKDEA 135
                D+     R  E      RA  GM FQ   LF  L   +NVT  L + +     + 
Sbjct: 69  -----DLMAMSARELETA----RAKFGMLFQGSALFDSLPIWRNVTFALTQGRMRDAAKM 119

Query: 136 VALAEKWLERVGL-LERRDHFPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALDPELV 194
             +A + LERVGL  +  D  P +LSGG Q+RVA+ARAIA  P ++ FDE T+ LDP   
Sbjct: 120 RKIAAENLERVGLGSQVLDLRPSELSGGMQKRVALARAIAPRPEIIFFDEPTTGLDPIRA 179

Query: 195 GEVLNVIKGLAED-GMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFE 247
             + ++I  L E+ G+T L +TH+M  A +++ ++  + QGRI   GP   L++
Sbjct: 180 DVINDLIVELVEELGVTALTITHDMASARKIAHRVAMLYQGRIVWSGPRDRLYD 233


Lambda     K      H
   0.320    0.138    0.392 

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: 161
Number of extensions: 12
Number of successful extensions: 4
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: 263
Length of database: 252
Length adjustment: 24
Effective length of query: 239
Effective length of database: 228
Effective search space:    54492
Effective search space used:    54492
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: 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