GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacK in Phaeobacter inhibens BS107

Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate GFF262 PGA1_c02740 sn-glycerol-3-phosphate import ATP-binding protein UgbC

Query= uniprot:D4GP39
         (383 letters)



>FitnessBrowser__Phaeo:GFF262
          Length = 348

 Score =  320 bits (819), Expect = 5e-92
 Identities = 185/364 (50%), Positives = 236/364 (64%), Gaps = 20/364 (5%)

Query: 1   MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60
           MA++TL+ V KVY +     + AV   S  I+DGEF+VLVGPSGCGKST LRM+AGLE +
Sbjct: 1   MAQVTLNSVRKVYPN----GVEAVTSSSFKIEDGEFVVLVGPSGCGKSTLLRMIAGLEDI 56

Query: 61  TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120
           TEG L + DRV+N V   DRDIAMVFQ+YALYPH +VR N+++GL+     P+ EI+Q+V
Sbjct: 57  TEGTLEIGDRVVNNVDPADRDIAMVFQNYALYPHMTVRKNIAYGLKNRK-TPEAEIKQKV 115

Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180
            E   ML + + LDRKP QLSGGQ+QRVA+GRAIVRDP +FL DEPLSNLDAKLR +MR 
Sbjct: 116 AEAAKMLNLEEYLDRKPSQLSGGQRQRVAMGRAIVRDPALFLFDEPLSNLDAKLRNQMRI 175

Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240
           E++ LQ  LGVT++YVTHDQ EAMTM DR+ VL+ G ++Q+GTP + YH P ++FVA F+
Sbjct: 176 EIKALQRRLGVTSIYVTHDQVEAMTMADRIIVLNGGRIEQIGTPSEIYHNPASVFVASFM 235

Query: 241 GEPSMNLFDGSL-SGDTFRGDGFDYPLSGATRDQLGGASGLTLGIRPEDVTVGERRSGQR 299
           G P MNL D ++ +G     DG      GA      GA  + LGIRPEDV +     G  
Sbjct: 236 GAPPMNLLDATIANGQVTLPDGVS---MGALDTSAQGA--VKLGIRPEDVQL--VAEGGL 288

Query: 300 TFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPEDAIHLFD 359
             D E  ++E  G    +H +      G  FT        V+ G    +S    AI LFD
Sbjct: 289 AIDVE--LIEELGAHRLLHGKL----GGQPFTIHVLKDIPVDPGTH-QISVDPAAICLFD 341

Query: 360 GETG 363
            E+G
Sbjct: 342 AESG 345


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: 427
Number of extensions: 22
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: 348
Length adjustment: 30
Effective length of query: 353
Effective length of database: 318
Effective search space:   112254
Effective search space used:   112254
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: 49 (23.5 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