GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacK in Magnetospirillum magneticum AMB-1

Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_011385004.1 AMB_RS13205 polyamine ABC transporter ATP-binding protein

Query= uniprot:D4GP39
         (383 letters)



>NCBI__GCF_000009985.1:WP_011385004.1
          Length = 379

 Score =  223 bits (569), Expect = 5e-63
 Identities = 127/316 (40%), Positives = 186/316 (58%), Gaps = 17/316 (5%)

Query: 19  GDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEGELRLEDRVLNGVSAQ 78
           GD  AVE + L I  GEF  L+G SGCGK+T LRM+AG E  T G + ++ + +  V   
Sbjct: 33  GDFTAVEHVDLAIHKGEFFSLLGASGCGKTTLLRMLAGFEIPTTGRILIDGQDVTEVPPY 92

Query: 79  DRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVEETTDMLGISDLLDRKPG 138
           +R + M+FQSYAL+PH SV  N++FGL++  GL    I+ +V    +++ +     RKP 
Sbjct: 93  ERPVNMMFQSYALFPHMSVADNIAFGLKQD-GLAKPVIKDKVAAALELVQMGRFSGRKPH 151

Query: 139 QLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQRLQGELGVTTVYVTH 198
           QLSGGQ+QRVAL R + ++P+V L+DEPL+ LD KLR   + EL  +Q  +G+T V VTH
Sbjct: 152 QLSGGQRQRVALARCLAKEPKVVLLDEPLAALDKKLREATQLELVNIQDRVGITFVMVTH 211

Query: 199 DQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGEPSMNLFDGSLSGDTFR 258
           DQ EAMTM  R+ V++ G ++QVG+P+D Y  P   FVA FIG  + N+F GS+ G    
Sbjct: 212 DQGEAMTMSSRIGVMNAGCIEQVGSPVDIYEYPGTRFVADFIG--AANMFQGSVRG---- 265

Query: 259 GDG--------FDYPLSGATRDQLGGASGLTLGIRPEDVTVGERR--SGQRTFDAEVVVV 308
           G+G         ++ LS      +   + +T+ +RPE V +   +  SG    +  V  +
Sbjct: 266 GEGALAIACPELEHDLSVTEAGAVAAGTPVTVMVRPEKVMIARDKPASGLNWAEGVVSDI 325

Query: 309 EPQGNENAVHLRFVDG 324
              G+ +  H+R   G
Sbjct: 326 AYLGDVSIYHVRLASG 341


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: 350
Number of extensions: 13
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: 379
Length adjustment: 30
Effective length of query: 353
Effective length of database: 349
Effective search space:   123197
Effective search space used:   123197
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 17 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