GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacJ in Sinorhizobium fredii NGR234

Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_164924745.1 NGR_RS30975 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= uniprot:D4GP38
         (383 letters)



>NCBI__GCF_000018545.1:WP_164924745.1
          Length = 355

 Score =  296 bits (757), Expect = 8e-85
 Identities = 167/371 (45%), Positives = 229/371 (61%), Gaps = 22/371 (5%)

Query: 1   MGQIQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDI 60
           M  + + ++TKR+G    +  LS  I+D EF+VLVGPSGCGKST LRMLAGLE  + GD+
Sbjct: 1   MTDVTIRNVTKRYGALTVIPQLSFRIEDGEFVVLVGPSGCGKSTLLRMLAGLEEISGGDL 60

Query: 61  YIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAE 120
            +G D +N R  + RD+A+VFQ+YALYPHMTV +N+ F L+  +    AE DERV + A 
Sbjct: 61  LMGADVINDRPAKERDMAIVFQNYALYPHMTVAENMGFALKLRKR-PRAEIDERVDKAAA 119

Query: 121 TLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNL 180
            LG+  LLDR P  LSGGQ+QRVA+GRAIVRDP+VFL DEPLSNLDAKLR +MR E++ L
Sbjct: 120 ILGLGKLLDRYPRALSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRAEIKAL 179

Query: 181 QDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMI 240
             +L +TTVYVTH+Q EAMTMAD+I VM++G ++Q+ +P E Y  P N+FVA FIG P +
Sbjct: 180 HQRLKITTVYVTHDQIEAMTMADKIVVMNEGRVEQMGTPLELYDRPANIFVAGFIGSPSM 239

Query: 241 NL----VRGTRSESTFVGEHFSYPLDEDVMESVDDRDDFVLGVRPEDIEVADAAPDDAAL 296
           N     V  T        E  + P+D     ++  R +   G+RPE +++ +        
Sbjct: 240 NFLPATVAATNGPLLKTPEGVALPIDGG--PTLTGRSEVTYGIRPEHLQLGETG------ 291

Query: 297 DDHDLQMDVTVVEPHGDQNVLHLSHPDQPSADDALQAVTEGMHLVTRGDRVTVTIPPDKI 356
               +  +V VVEP G +  L+++          + AV      V  G+++ +T      
Sbjct: 292 ----IPAEVVVVEPTGSETQLYVT-----VGGREVVAVLRDRVDVRPGEKIWLTPRKGCA 342

Query: 357 HLFDAETGTAV 367
           HLFD  TG  +
Sbjct: 343 HLFDPNTGARI 353


Lambda     K      H
   0.317    0.135    0.386 

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: 370
Number of extensions: 16
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: 383
Length of database: 355
Length adjustment: 30
Effective length of query: 353
Effective length of database: 325
Effective search space:   114725
Effective search space used:   114725
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 (21.6 bits)
S2: 49 (23.5 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