GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacK in Lactobacillus pobuzihii E100301

Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_017868944.1 LACPOB_RS0111380 ABC transporter ATP-binding protein

Query= uniprot:D4GP39
         (383 letters)



>NCBI__GCF_000349725.1:WP_017868944.1
          Length = 372

 Score =  249 bits (635), Expect = 1e-70
 Identities = 145/369 (39%), Positives = 209/369 (56%), Gaps = 14/369 (3%)

Query: 8   DVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEGELRL 67
           ++  +Y    G     +++I+L I D +F+ +VGPSGCGKST LR  AGLE + +GE+ +
Sbjct: 5   EIKHLYKKYPGRSNYTLKDINLSIKDKQFVAIVGPSGCGKSTLLRCFAGLEEINKGEVLV 64

Query: 68  EDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVEETTDML 127
             +  + +  ++R++AMVFQ YALYPH +V  NM++ L+ +     + I Q+V E  + L
Sbjct: 65  NGKNFDKIDPRNRNVAMVFQDYALYPHMTVFKNMAYNLKIAKK-DKETIEQKVTEAAEKL 123

Query: 128 GISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQRLQG 187
            ++D L +KP QLSGGQ+QRVALGRA+VRDPE+FLMDEPLSNLDAKLR + R ++  L  
Sbjct: 124 KLTDYLQQKPAQLSGGQRQRVALGRAMVRDPEIFLMDEPLSNLDAKLRVKTRQDIIDLHR 183

Query: 188 ELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGEPSMNL 247
           +LG  T+YVTHDQ EAM + D++ V+ DG L Q GTP + Y  P+N+FVA FIG PSMN+
Sbjct: 184 QLGTITMYVTHDQAEAMALADQIVVMRDGILMQTGTPAELYDDPHNIFVARFIGSPSMNI 243

Query: 248 FDGSL-SGDTFRGDGFDYPLSGATRDQL--GGASGLTLGIRPEDVTV-------GERRSG 297
           F G L S   F+     Y L       L       + +G RPE            E    
Sbjct: 244 FRGFLDSKAQFKVGKTTYNLKNIVPKSLLPVDEQEIFIGFRPEQTRPLLPSEEGKENDKD 303

Query: 298 QRTFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPEDAIHL 357
           + TF A++   E  G    ++L   +     Q      G        + T+      ++ 
Sbjct: 304 KFTFKAQLNYAEYMGAYTLLYLEAHERSIVAQIYRKIEGSPH---NRQVTMEVTPKDLYF 360

Query: 358 FDGETGDAL 366
           F+ +TG  +
Sbjct: 361 FNADTGQRM 369


Lambda     K      H
   0.316    0.136    0.384 

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: 358
Number of extensions: 13
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: 372
Length adjustment: 30
Effective length of query: 353
Effective length of database: 342
Effective search space:   120726
Effective search space used:   120726
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: 42 (22.0 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