GapMind for catabolism of small carbon sources

 

Alignments for a candidate for musK in Herbaspirillum seropedicae SmR1

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate HSERO_RS18940 HSERO_RS18940 sn-glycerol-3-phosphate ABC transporter ATP-binding protein

Query= BRENDA::Q8NMV1
         (376 letters)



>FitnessBrowser__HerbieS:HSERO_RS18940
          Length = 364

 Score =  304 bits (778), Expect = 3e-87
 Identities = 177/386 (45%), Positives = 229/386 (59%), Gaps = 34/386 (8%)

Query: 1   MATVTFKDASLSYPGAKEPT--VKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVT 58
           MA +  K    +Y    +    +   + EIADGEF+V+VGPSGCGKST LRM+AGLE ++
Sbjct: 1   MAAIHLKQVRKTYGAGTKAVDVIHGIDAEIADGEFIVMVGPSGCGKSTLLRMVAGLEEIS 60

Query: 59  DGAIFIGDKDVTHVAPRDRDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDE 118
            G I IGD+ V  + P++RDIAMVFQNYALYPHMTV +NM + LKI G S+ EI+ RV  
Sbjct: 61  SGQIVIGDRVVNDLEPKERDIAMVFQNYALYPHMTVYQNMAYGLKIQGLSKSEIDARVQR 120

Query: 119 AAATLGLTEFLERKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQI 178
           AAA L L   LER P+ LSGGQRQRVAMGRAIVR P VFL DEPLSNLDAKLRVQ R +I
Sbjct: 121 AAAILELGALLERTPRQLSGGQRQRVAMGRAIVRKPAVFLFDEPLSNLDAKLRVQMRLEI 180

Query: 179 AALQRKLGVTTVYVTHDQTEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGS 238
             L   L  T++YVTHDQ EA+T+G R+ V+  G  +Q+G P E+Y RPA  FVA FIGS
Sbjct: 181 QKLHASLRTTSLYVTHDQVEAMTLGQRMIVMNRGVAEQIGTPAEVYARPATTFVASFIGS 240

Query: 239 PAMNL---------GTFSVKDGDATSGHARIKLSPETLAAMTPEDNGRITIGFRPEALEI 289
           P MNL          +F V  G+A+     I   P+ L     ++     +G RPE L  
Sbjct: 241 PPMNLLQGKLSADGASFEVSKGNASD----ILRLPQPLTGAAGQER---ILGVRPEHLLP 293

Query: 290 IPEGESTDLSIPIKLDFVEELGSDSFLYGKLVGEGDLGSSSEDVPESGQIVVRAAPNAAP 349
           I +G +  LS+ ++L  VE LG++  ++ +  G+               +V+R   N   
Sbjct: 294 ILDGSAAQLSLEVEL--VEALGAELLVHARCGGQA--------------LVLRCPANVQV 337

Query: 350 APGSVFHARIVEGGQHNFSASTGKRL 375
             G    A    G  H F   + +R+
Sbjct: 338 RTGQRIGASFGAGDVHWFDVKSTRRI 363


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: 350
Number of extensions: 10
Number of successful extensions: 1
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: 364
Length adjustment: 30
Effective length of query: 346
Effective length of database: 334
Effective search space:   115564
Effective search space used:   115564
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 17 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