GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc04256 in Herbaspirillum seropedicae SmR1

Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate HSERO_RS18940 HSERO_RS18940 sn-glycerol-3-phosphate ABC transporter ATP-binding protein

Query= reanno::Smeli:SMc04256
         (361 letters)



>FitnessBrowser__HerbieS:HSERO_RS18940
          Length = 364

 Score =  305 bits (781), Expect = 1e-87
 Identities = 167/366 (45%), Positives = 237/366 (64%), Gaps = 8/366 (2%)

Query: 1   MTSVSVRDLSLNFGA----VTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVS 56
           M ++ ++ +   +GA    V V+  ++ +I  GEF+V++G SGCGKSTLL  +AGL ++S
Sbjct: 1   MAAIHLKQVRKTYGAGTKAVDVIHGIDAEIADGEFIVMVGPSGCGKSTLLRMVAGLEEIS 60

Query: 57  DGQIFIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKR 116
            GQI I DR V   EPK+R I MVFQ+YALYP MTV +N+++GLK+  +  +EI+ RV+R
Sbjct: 61  SGQIVIGDRVVNDLEPKERDIAMVFQNYALYPHMTVYQNMAYGLKIQGLSKSEIDARVQR 120

Query: 117 ASEILQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEI 176
           A+ IL++  LL+R P +LSGGQRQRVA+GRA+VR   VFLFDEPLSNLDAKLR ++R+EI
Sbjct: 121 AAAILELGALLERTPRQLSGGQRQRVAMGRAIVRKPAVFLFDEPLSNLDAKLRVQMRLEI 180

Query: 177 KRLHQSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGS 236
           ++LH SL+ T +YVTHDQ+EA+TL  R+ VM  GV +Q+  P  +Y  P   FVA FIGS
Sbjct: 181 QKLHASLRTTSLYVTHDQVEAMTLGQRMIVMNRGVAEQIGTPAEVYARPATTFVASFIGS 240

Query: 237 PSMNFFRGEVEPKDGRSFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEARDG 296
           P MN  +G++   DG SF  + G A D+   P       GQ+ +LG+RPEH+      DG
Sbjct: 241 PPMNLLQGKLS-ADGASFEVSKGNASDILRLPQPLTGAAGQERILGVRPEHLL--PILDG 297

Query: 297 EPTHQAV-VDIEEPMGADNLLWLTFAGQSMSVRIAGQRRYPPGSTVRLSFDMGVASIFDA 355
                ++ V++ E +GA+ L+     GQ++ +R     +   G  +  SF  G    FD 
Sbjct: 298 SAAQLSLEVELVEALGAELLVHARCGGQALVLRCPANVQVRTGQRIGASFGAGDVHWFDV 357

Query: 356 ESENRL 361
           +S  R+
Sbjct: 358 KSTRRI 363


Lambda     K      H
   0.320    0.137    0.392 

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: 357
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: 361
Length of database: 364
Length adjustment: 29
Effective length of query: 332
Effective length of database: 335
Effective search space:   111220
Effective search space used:   111220
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