GapMind for catabolism of small carbon sources

 

Alignments for a candidate for msiK in Herbaspirillum seropedicae SmR1

Align MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized)
to candidate HSERO_RS18940 HSERO_RS18940 sn-glycerol-3-phosphate ABC transporter ATP-binding protein

Query= TCDB::P96483
         (377 letters)



>FitnessBrowser__HerbieS:HSERO_RS18940
          Length = 364

 Score =  301 bits (772), Expect = 1e-86
 Identities = 183/383 (47%), Positives = 237/383 (61%), Gaps = 28/383 (7%)

Query: 1   MATVTFDKATRIYPGSDKPAVDQL---DIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDV 57
           MA +   +  + Y G+   AVD +   D  I DGEF+V+VGPSGCGKST LRM+AGLE++
Sbjct: 1   MAAIHLKQVRKTY-GAGTKAVDVIHGIDAEIADGEFIVMVGPSGCGKSTLLRMVAGLEEI 59

Query: 58  NGGAIRIGDRDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVE 117
           + G I IGDR V  L PK+RDIAMVFQNYALYPHMTV  NM + LKI G+ K+EI  +V+
Sbjct: 60  SSGQIVIGDRVVNDLEPKERDIAMVFQNYALYPHMTVYQNMAYGLKIQGLSKSEIDARVQ 119

Query: 118 EAAKILDLTQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQ 177
            AA IL+L   L+R P+ LSGGQRQRVAMGRAIVR+P VFL DEPLSNLDAKLRV  R +
Sbjct: 120 RAAAILELGALLERTPRQLSGGQRQRVAMGRAIVRKPAVFLFDEPLSNLDAKLRVQMRLE 179

Query: 178 IASLQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIG 237
           I  L   L  T++YVTHDQVEAMT+G R+ V+  G+ +Q+ +P  +Y +PA  FVA FIG
Sbjct: 180 IQKLHASLRTTSLYVTHDQVEAMTLGQRMIVMNRGVAEQIGTPAEVYARPATTFVASFIG 239

Query: 238 SPAMNLVEVPITDGGVKF----GN-SVVPVNREALSAADKGDRTVTVGVRPEHFDVVELG 292
           SP MNL++  ++  G  F    GN S +    + L+ A   +R   +GVRPEH   +  G
Sbjct: 240 SPPMNLLQGKLSADGASFEVSKGNASDILRLPQPLTGAAGQER--ILGVRPEHLLPILDG 297

Query: 293 GAVAASLSKDSADAPAGLAVSVNVVEELGADGYVYGTAEVGGEVKDLVVRVNGRQVPEKG 352
            A             A L++ V +VE LGA+  V+  A  GG+   LV+R         G
Sbjct: 298 SA-------------AQLSLEVELVEALGAELLVH--ARCGGQA--LVLRCPANVQVRTG 340

Query: 353 STLHVVPRPGETHVFSTSTGERL 375
             +      G+ H F   +  R+
Sbjct: 341 QRIGASFGAGDVHWFDVKSTRRI 363


Lambda     K      H
   0.317    0.135    0.379 

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: 377
Number of extensions: 13
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: 377
Length of database: 364
Length adjustment: 30
Effective length of query: 347
Effective length of database: 334
Effective search space:   115898
Effective search space used:   115898
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