GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Rhodobacter johrii JA192

Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate WP_069331237.1 C8J29_RS14155 sn-glycerol-3-phosphate import ATP-binding protein UgpC

Query= reanno::WCS417:GFF4321
         (386 letters)



>NCBI__GCF_003046325.1:WP_069331237.1
          Length = 349

 Score =  316 bits (810), Expect = 6e-91
 Identities = 182/366 (49%), Positives = 242/366 (66%), Gaps = 18/366 (4%)

Query: 1   MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60
           MA + LR+V K+Y +GL + +  ++L I +GEF+++VGPSGCGKSTL+  +AGLE IT G
Sbjct: 1   MAEISLRDVRKSY-SGL-EVIHGVDLEIADGEFVVIVGPSGCGKSTLLRMVAGLEEITAG 58

Query: 61  AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120
            I IG + V+ + P++RDIAMVFQ+YALYP M+VREN+ +GL+I K+ +A+I+  VAR A
Sbjct: 59  EIAIGGRVVNRLEPRERDIAMVFQNYALYPHMTVRENMAYGLRIAKLSKAEIEERVARSA 118

Query: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180
           K+L++  LL+RKP QLSGGQ+QRVAMGRAL R P  +L DEPLSNLDAKLRV+MR ++K 
Sbjct: 119 KMLELGQLLDRKPRQLSGGQRQRVAMGRALVRNPAAFLLDEPLSNLDAKLRVQMRLQIKE 178

Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240
           + + ++TT++YVTHDQ+EAMTL D++ VM  G+ +Q  TP EIY+ PA  FVA FIGSP 
Sbjct: 179 LQRTVRTTSIYVTHDQVEAMTLADRLVVMNAGVAEQIATPAEIYDRPATTFVAGFIGSPA 238

Query: 241 MNFVPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGEGDS 300
           MN +P R     G   AL  +GQ    LA+    AG   RD+ILG+RPE +  A   G  
Sbjct: 239 MNMLPAR-----GLGDALEVAGQ---RLAV-PAPAG---RDLILGIRPEHLHPA---GPE 283

Query: 301 ASSIRAEVQVTEPTGPDTLVFVQLNDTKVCCRLAPDVAP-QVGETLTLQFDPSKVLLFDA 359
                  VQ  E  G D      L D        P  AP +  + L +  D + + LFDA
Sbjct: 284 EPGFELHVQAVEWLGADAFAHGSLADGTDLVLRTPGKAPVRERDRLKVAPDAAALHLFDA 343

Query: 360 NTGERL 365
            TG RL
Sbjct: 344 GTGRRL 349


Lambda     K      H
   0.318    0.135    0.382 

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: 388
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: 386
Length of database: 349
Length adjustment: 30
Effective length of query: 356
Effective length of database: 319
Effective search space:   113564
Effective search space used:   113564
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 (21.7 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