GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacJ in Thiothrix lacustris DSM 21227

Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_028488909.1 Q394_RS0108480 spermidine/putrescine ABC transporter ATP-binding protein PotA

Query= uniprot:D4GP38
         (383 letters)



>NCBI__GCF_000621325.1:WP_028488909.1
          Length = 369

 Score =  227 bits (579), Expect = 4e-64
 Identities = 130/300 (43%), Positives = 183/300 (61%), Gaps = 18/300 (6%)

Query: 4   IQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIG 63
           + L++++KRF     + D +L I D EF  ++GPSGCGK+T LR++AG E P  G I + 
Sbjct: 7   LTLSNISKRFASQEVLSDFNLTIQDGEFFTILGPSGCGKTTVLRLIAGFEQPNEGQILLN 66

Query: 64  GDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAETLG 123
           GD +     + R    VFQ YAL+PH+TV  N+ FGL+        +  +  V VA+ L 
Sbjct: 67  GDDIARIPAEKRPFNTVFQSYALFPHLTVFDNVAFGLK----MAGVDVQDIAVRVADALA 122

Query: 124 IADLLD---RKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNL 180
           I  L +   RKP +LSGGQ+QRVA+ RA+V  P++ L+DE LS LD KLR +M+ EL+ L
Sbjct: 123 IVRLSEFATRKPHQLSGGQKQRVAIARAVVNRPKILLLDESLSALDYKLRQQMQLELKQL 182

Query: 181 QDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMI 240
           Q QL +T VYVTH+Q EA++M+DRI VM +G+ QQV +P E Y  P NLFVA+FIGE  I
Sbjct: 183 QRQLGITFVYVTHDQEEALSMSDRILVMHNGQAQQVGTPREIYESPRNLFVAQFIGE--I 240

Query: 241 NLVRGTRSESTFVGEHFSYPLDEDVMESVDDRDDFVLG------VRPEDIEVADAAPDDA 294
           N+  G   ++  +GE+        V+  +     F +G      +RPED+ + D  PD A
Sbjct: 241 NVFDGEIVQA--LGEYQYEASINGVVREIRCDHRFAVGDKVHVMLRPEDLRI-DCRPDVA 297


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: 348
Number of extensions: 9
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: 383
Length of database: 369
Length adjustment: 30
Effective length of query: 353
Effective length of database: 339
Effective search space:   119667
Effective search space used:   119667
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: 50 (23.9 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