GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Rhodobacter johrii JA192

Align Trehalose import ATP-binding protein SugC; EC 7.5.2.- (characterized)
to candidate WP_069331237.1 C8J29_RS14155 sn-glycerol-3-phosphate import ATP-binding protein UgpC

Query= SwissProt::P9WQI3
         (393 letters)



>NCBI__GCF_003046325.1:WP_069331237.1
          Length = 349

 Score =  350 bits (899), Expect = e-101
 Identities = 201/389 (51%), Positives = 259/389 (66%), Gaps = 42/389 (10%)

Query: 1   MAEIVLDHVNKSYPDGHTAVRDLNLTIADGEFLILVGPSGCGKTTTLNMIAGLEDISSGE 60
           MAEI L  V KSY  G   +  ++L IADGEF+++VGPSGCGK+T L M+AGLE+I++GE
Sbjct: 1   MAEISLRDVRKSY-SGLEVIHGVDLEIADGEFVVIVGPSGCGKSTLLRMVAGLEEITAGE 59

Query: 61  LRIAGERVNEKAPKDRDIAMVFQSYALYPHMTVRQNIAFPLTLAKMRKADIAQKVSETAK 120
           + I G  VN   P++RDIAMVFQ+YALYPHMTVR+N+A+ L +AK+ KA+I ++V+ +AK
Sbjct: 60  IAIGGRVVNRLEPRERDIAMVFQNYALYPHMTVRENMAYGLRIAKLSKAEIEERVARSAK 119

Query: 121 ILDLTNLLDRKPSQLSGGQRQRVAMGRAIVRHPKAFLMDEPLSNLDAKLRVQMRGEIAQL 180
           +L+L  LLDRKP QLSGGQRQRVAMGRA+VR+P AFL+DEPLSNLDAKLRVQMR +I +L
Sbjct: 120 MLELGQLLDRKPRQLSGGQRQRVAMGRALVRNPAAFLLDEPLSNLDAKLRVQMRLQIKEL 179

Query: 181 QRRLGTTTVYVTHDQTEAMTLGDRVVVMYGGIAQQIGTPEELYERPANLFVAGFIGSPAM 240
           QR + TT++YVTHDQ EAMTL DR+VVM  G+A+QI TP E+Y+RPA  FVAGFIGSPAM
Sbjct: 180 QRTVRTTSIYVTHDQVEAMTLADRLVVMNAGVAEQIATPAEIYDRPATTFVAGFIGSPAM 239

Query: 241 NFFPARLTAIGLTLPFGEVTLAPEVQGVIAAHPKP--ENVIVGVRPEHIQDAALIDAYQR 298
           N  PAR    GL    G+   A EV G   A P P   ++I+G+RPEH+  A   +    
Sbjct: 240 NMLPAR----GL----GD---ALEVAGQRLAVPAPAGRDLILGIRPEHLHPAGPEEP--- 285

Query: 299 IRALTFQVKVNLVESLGADKYLYFTTESPAVHSVQLDELAEVEGESALHENQFVARVPAE 358
                F++ V  VE LGAD + +                      S       V R P +
Sbjct: 286 ----GFELHVQAVEWLGADAFAH---------------------GSLADGTDLVLRTPGK 320

Query: 359 SKVAIGQSVELAFDTARLAVFDADSGANL 387
           + V     +++A D A L +FDA +G  L
Sbjct: 321 APVRERDRLKVAPDAAALHLFDAGTGRRL 349


Lambda     K      H
   0.319    0.135    0.377 

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: 434
Number of extensions: 18
Number of successful extensions: 4
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: 393
Length of database: 349
Length adjustment: 30
Effective length of query: 363
Effective length of database: 319
Effective search space:   115797
Effective search space used:   115797
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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