GapMind for catabolism of small carbon sources

 

Alignments for a candidate for musK in Rhodobacter johrii JA192

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_069331237.1 C8J29_RS14155 sn-glycerol-3-phosphate import ATP-binding protein UgpC

Query= BRENDA::Q8NMV1
         (376 letters)



>NCBI__GCF_003046325.1:WP_069331237.1
          Length = 349

 Score =  316 bits (810), Expect = 5e-91
 Identities = 186/375 (49%), Positives = 237/375 (63%), Gaps = 26/375 (6%)

Query: 1   MATVTFKDASLSYPGAKEPTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDG 60
           MA ++ +D   SY G +   +   +LEIADGEF+V+VGPSGCGKST LRM+AGLE +T G
Sbjct: 1   MAEISLRDVRKSYSGLE--VIHGVDLEIADGEFVVIVGPSGCGKSTLLRMVAGLEEITAG 58

Query: 61  AIFIGDKDVTHVAPRDRDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAA 120
            I IG + V  + PR+RDIAMVFQNYALYPHMTV ENM + L+IA  S+ EI +RV  +A
Sbjct: 59  EIAIGGRVVNRLEPRERDIAMVFQNYALYPHMTVRENMAYGLRIAKLSKAEIEERVARSA 118

Query: 121 ATLGLTEFLERKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAA 180
             L L + L+RKP+ LSGGQRQRVAMGRA+VRNP  FL+DEPLSNLDAKLRVQ R QI  
Sbjct: 119 KMLELGQLLDRKPRQLSGGQRQRVAMGRALVRNPAAFLLDEPLSNLDAKLRVQMRLQIKE 178

Query: 181 LQRKLGVTTVYVTHDQTEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPA 240
           LQR +  T++YVTHDQ EA+T+ DR+ V+  G  +Q+  P E+YDRPA  FVAGFIGSPA
Sbjct: 179 LQRTVRTTSIYVTHDQVEAMTLADRLVVMNAGVAEQIATPAEIYDRPATTFVAGFIGSPA 238

Query: 241 MNLGTFSVKDGDATSGHARIKLSPETLAAMTPEDNGRITIGFRPEALEIIPEGESTDLSI 300
           MN+   +   GDA      ++++ + LA   P     I +G RPE L   P G   +   
Sbjct: 239 MNM-LPARGLGDA------LEVAGQRLAVPAPAGRDLI-LGIRPEHLH--PAGPE-EPGF 287

Query: 301 PIKLDFVEELGSDSFLYGKLVGEGDLGSSSEDVPESGQIVVRAAPNAAPAPGSVFHARIV 360
            + +  VE LG+D+F +G L    DL      +   G+  VR       AP +       
Sbjct: 288 ELHVQAVEWLGADAFAHGSLADGTDL-----VLRTPGKAPVRERDRLKVAPDA------- 335

Query: 361 EGGQHNFSASTGKRL 375
               H F A TG+RL
Sbjct: 336 -AALHLFDAGTGRRL 349


Lambda     K      H
   0.316    0.135    0.380 

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: 389
Number of extensions: 17
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: 376
Length of database: 349
Length adjustment: 29
Effective length of query: 347
Effective length of database: 320
Effective search space:   111040
Effective search space used:   111040
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 (21.6 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