GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21725 in Rhodobacter viridis JA737

Align ABC transporter for D-Glucosamine, putative ATPase component (characterized)
to candidate WP_110806538.1 C8J30_RS14405 ABC transporter ATP-binding protein

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



>NCBI__GCF_003217355.1:WP_110806538.1
          Length = 358

 Score =  159 bits (401), Expect = 1e-43
 Identities = 101/255 (39%), Positives = 139/255 (54%), Gaps = 21/255 (8%)

Query: 13  LLDIRGLRKQYGPLE-----VLKGVDLSMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQG 67
           LLDIR  R+ +   E      L GVDL++  G  VTL+G SG GKTTLLR +   EE   
Sbjct: 6   LLDIRAARRLFTTPEGKSFAALDGVDLAVDEGEFVTLLGPSGCGKTTLLRAIAGFEELDE 65

Query: 68  GQIMLDGESIGYDDIDGKRVRHPEKVIARHRAMTGMAFQQFNLFPHLTALQNVTLGLLKV 127
           G I LDG      D+ G         +  HR      FQ + LFPH++  +NV   L +V
Sbjct: 66  GVIRLDGA-----DLSG---------LPPHRRPVNTVFQSYALFPHMSVARNVGYAL-EV 110

Query: 128 KKLPKDEAVALAEKWLERVGLLERRDHFPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTS 187
           +  P+ E  A     LE+VGL       P QLSGGQ+QRVA+ARAI   P L+L DE  S
Sbjct: 111 QGAPRAEREAEVAAALEKVGLAGLGTRRPAQLSGGQRQRVALARAIVAKPRLLLLDEPLS 170

Query: 188 ALDPELVGEVLNVIKGLAED-GMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELF 246
           ALD  L  ++   +K L    G+  + VTH+   A  +SD+IV +  G++E+  PP+E++
Sbjct: 171 ALDRNLRQQMQFELKDLQHRLGIAFVFVTHDQEEALTMSDRIVVLRAGKVEQAAPPREIY 230

Query: 247 ERPQSPRLAEFLKNT 261
             P++  +AEF+  T
Sbjct: 231 RHPKTRFVAEFIGET 245


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: 244
Number of extensions: 8
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: 358
Length adjustment: 27
Effective length of query: 236
Effective length of database: 331
Effective search space:    78116
Effective search space used:    78116
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: 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