GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacJ in Marivita geojedonensis DPG-138

Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_085637757.1 MGEO_RS11955 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= uniprot:D4GP38
         (383 letters)



>NCBI__GCF_002115805.1:WP_085637757.1
          Length = 365

 Score =  281 bits (720), Expect = 2e-80
 Identities = 157/317 (49%), Positives = 209/317 (65%), Gaps = 15/317 (4%)

Query: 4   IQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIG 63
           + + +L K +G T  + D+++ I+  +FLVLVGPSGCGKST L  +AGLE  T G I IG
Sbjct: 5   LDIKNLYKSYGTTEILKDINVSIEPGDFLVLVGPSGCGKSTLLNCIAGLEPITGGSINIG 64

Query: 64  GDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAETLG 123
           G  M +  P++RDIAMVFQ YALYP MTV +NI FG++   G   A +D ++ +VA+ L 
Sbjct: 65  GKDMTHVSPKDRDIAMVFQSYALYPTMTVAKNITFGMKVR-GVDQATQDRKLAQVAQQLQ 123

Query: 124 IADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNLQDQ 183
           I  LL+R+P +LSGGQ+QRVA+GRA+VRDP++FL DEPLSNLDAKLR EMRTE+++L   
Sbjct: 124 IEPLLNRRPGQLSGGQRQRVAMGRALVRDPKLFLFDEPLSNLDAKLRVEMRTEIKSLHHN 183

Query: 184 LAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMINLV 243
           L  + VYVTH+Q EAMT+A +I VM  G +QQ+ SP E Y+ P NLFVA+F+G P +NL+
Sbjct: 184 LGASMVYVTHDQIEAMTLATKIVVMKGGVIQQIGSPAEIYNRPANLFVADFMGSPAMNLI 243

Query: 244 --------RGTRSESTFVGEHFSYPLDEDVMESVDDRDDFVLGVRPEDIEVADAAPDDAA 295
                    GTR E T        P+     ++ D  +D +LGVRPEDI   D    +AA
Sbjct: 244 PAKAHRADEGTRIEIT---RKSGEPIVLTDTKNRDLPEDVILGVRPEDIADPDLRGAEAA 300

Query: 296 LDDHDLQMDVTVVEPHG 312
                L   + +VEP G
Sbjct: 301 QAAECL---IDMVEPAG 314


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: 343
Number of extensions: 10
Number of successful extensions: 3
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: 365
Length adjustment: 30
Effective length of query: 353
Effective length of database: 335
Effective search space:   118255
Effective search space used:   118255
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 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