GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Herbaspirillum seropedicae SmR1

Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate HSERO_RS18940 HSERO_RS18940 sn-glycerol-3-phosphate ABC transporter ATP-binding protein

Query= TCDB::P54933
         (332 letters)



>FitnessBrowser__HerbieS:HSERO_RS18940
          Length = 364

 Score =  307 bits (786), Expect = 3e-88
 Identities = 173/356 (48%), Positives = 223/356 (62%), Gaps = 32/356 (8%)

Query: 1   MGKITLRNVQKRFGEAV----VIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVS 56
           M  I L+ V+K +G       VI  +D +I DGEF+V VGPSGCGKSTLLR++AGLE++S
Sbjct: 1   MAAIHLKQVRKTYGAGTKAVDVIHGIDAEIADGEFIVMVGPSGCGKSTLLRMVAGLEEIS 60

Query: 57  DGQIMIDGRDATEMPPAKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRVSN 116
            GQI+I  R   ++ P +R +AMVFQ+YALYPHMTV +N+A+ L++  +   EI+ RV  
Sbjct: 61  SGQIVIGDRVVNDLEPKERDIAMVFQNYALYPHMTVYQNMAYGLKIQGLSKSEIDARVQR 120

Query: 117 AAKILNLTNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLEI 176
           AA IL L   L+R P QLSGGQRQRVA+GRAIVR+PA FLFDEPLSNLDA LRV MRLEI
Sbjct: 121 AAAILELGALLERTPRQLSGGQRQRVAMGRAIVRKPAVFLFDEPLSNLDAKLRVQMRLEI 180

Query: 177 TELHQSLETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLTLYRNPANLFVAGFIGS 236
            +LH SL TT +YVTHDQVEAMT+  +++V+N G  EQ+G+P  +Y  PA  FVA FIGS
Sbjct: 181 QKLHASLRTTSLYVTHDQVEAMTLGQRMIVMNRGVAEQIGTPAEVYARPATTFVASFIGS 240

Query: 237 PKMNLIEGP--------EAAKHGATTI-----------------GIRPEHI--DLSREAG 269
           P MNL++G         E +K  A+ I                 G+RPEH+   L   A 
Sbjct: 241 PPMNLLQGKLSADGASFEVSKGNASDILRLPQPLTGAAGQERILGVRPEHLLPILDGSAA 300

Query: 270 AWEGEVGVSEHLGSDTFLHVHVAGMPTLTVRTGGEFGVHHGDRVWLTPQADKIHRF 325
               EV + E LG++  +H    G   L +R      V  G R+  +  A  +H F
Sbjct: 301 QLSLEVELVEALGAELLVHARCGGQ-ALVLRCPANVQVRTGQRIGASFGAGDVHWF 355


Lambda     K      H
   0.320    0.137    0.400 

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: 360
Number of extensions: 14
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: 332
Length of database: 364
Length adjustment: 29
Effective length of query: 303
Effective length of database: 335
Effective search space:   101505
Effective search space used:   101505
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 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