GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacK in Rhodobacter johrii JA192

Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_069331237.1 C8J29_RS14155 sn-glycerol-3-phosphate import ATP-binding protein UgpC

Query= uniprot:D4GP39
         (383 letters)



>NCBI__GCF_003046325.1:WP_069331237.1
          Length = 349

 Score =  298 bits (762), Expect = 2e-85
 Identities = 174/369 (47%), Positives = 228/369 (61%), Gaps = 23/369 (6%)

Query: 1   MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60
           MA ++L DV K Y+      +  +  + L+I DGEF+V+VGPSGCGKST LRM+AGLE +
Sbjct: 1   MAEISLRDVRKSYSG-----LEVIHGVDLEIADGEFVVIVGPSGCGKSTLLRMVAGLEEI 55

Query: 61  TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120
           T GE+ +  RV+N +  ++RDIAMVFQ+YALYPH +VR NM++GL  +  L   EI +RV
Sbjct: 56  TAGEIAIGGRVVNRLEPRERDIAMVFQNYALYPHMTVRENMAYGLRIAK-LSKAEIEERV 114

Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180
             +  ML +  LLDRKP QLSGGQ+QRVA+GRA+VR+P  FL+DEPLSNLDAKLR +MR 
Sbjct: 115 ARSAKMLELGQLLDRKPRQLSGGQRQRVAMGRALVRNPAAFLLDEPLSNLDAKLRVQMRL 174

Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240
           +++ LQ  +  T++YVTHDQ EAMT+ DR+ V++ G  +Q+ TP + Y RP   FVAGFI
Sbjct: 175 QIKELQRTVRTTSIYVTHDQVEAMTLADRLVVMNAGVAEQIATPAEIYDRPATTFVAGFI 234

Query: 241 GEPSMNLFDGSLSGDTFR--GDGFDYPLSGATRDQLGGASGLTLGIRPEDV-TVGERRSG 297
           G P+MN+      GD     G     P + A RD       L LGIRPE +   G    G
Sbjct: 235 GSPAMNMLPARGLGDALEVAGQRLAVP-APAGRD-------LILGIRPEHLHPAGPEEPG 286

Query: 298 QRTFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPEDAIHL 357
              F+  V  VE  G +   H    D   GT     T G++ V   DR  V+    A+HL
Sbjct: 287 ---FELHVQAVEWLGADAFAHGSLAD---GTDLVLRTPGKAPVRERDRLKVAPDAAALHL 340

Query: 358 FDGETGDAL 366
           FD  TG  L
Sbjct: 341 FDAGTGRRL 349


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: 410
Number of extensions: 24
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: 349
Length adjustment: 30
Effective length of query: 353
Effective length of database: 319
Effective search space:   112607
Effective search space used:   112607
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 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