GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21216 in Rhodobacter johrii JA192

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

Query= reanno::Smeli:SM_b21216
         (360 letters)



>NCBI__GCF_003046325.1:WP_069331237.1
          Length = 349

 Score =  322 bits (825), Expect = 9e-93
 Identities = 171/358 (47%), Positives = 236/358 (65%), Gaps = 10/358 (2%)

Query: 1   MSALEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDI 60
           M+ + +R++RK Y  +E + G+D+ +  GEF+V++G SGCGKSTLL ++AGL E + G+I
Sbjct: 1   MAEISLRDVRKSYSGLEVIHGVDLEIADGEFVVIVGPSGCGKSTLLRMVAGLEEITAGEI 60

Query: 61  LIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARL 120
            IG R V  + P++RDIAMVFQ+YALYP+++V  N+ +GL + ++ +AE ++ V  +A++
Sbjct: 61  AIGGRVVNRLEPRERDIAMVFQNYALYPHMTVRENMAYGLRIAKLSKAEIEERVARSAKM 120

Query: 121 LQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLH 180
           L++  LLDRKP QLSGGQRQRVA+GRALVRNP  FL DEPLSNLDAKLR++MR ++K L 
Sbjct: 121 LELGQLLDRKPRQLSGGQRQRVAMGRALVRNPAAFLLDEPLSNLDAKLRVQMRLQIKELQ 180

Query: 181 QMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMN 240
           + +RTT +YVTHDQ+EAMTLA R+ VM  G  EQ+A P E+YDRPAT +VAGF+GSP MN
Sbjct: 181 RTVRTTSIYVTHDQVEAMTLADRLVVMNAGVAEQIATPAEIYDRPATTFVAGFIGSPAMN 240

Query: 241 ILDAEMTANGLKIEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLAAGSEAQRLTASV 300
           +L A    + L++ G    +P P        AGR + +GIRPE L   AG E       V
Sbjct: 241 MLPARGLGDALEVAGQRLAVPAP--------AGRDLILGIRPEHLH-PAGPEEPGFELHV 291

Query: 301 EVVELTGPELVTTATVG-SQRITACLPPRTAVGMGSAHAFTFDGTALHLFDPESGRSL 357
           + VE  G +     ++     +    P +  V          D  ALHLFD  +GR L
Sbjct: 292 QAVEWLGADAFAHGSLADGTDLVLRTPGKAPVRERDRLKVAPDAAALHLFDAGTGRRL 349


Lambda     K      H
   0.320    0.136    0.385 

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: 378
Number of extensions: 18
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: 360
Length of database: 349
Length adjustment: 29
Effective length of query: 331
Effective length of database: 320
Effective search space:   105920
Effective search space used:   105920
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