GapMind for catabolism of small carbon sources

 

Aligments for a candidate for SMc04256 in Herbaspirillum seropedicae SmR1

Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate HSERO_RS16715 HSERO_RS16715 sugar ABC transporter ATP-binding protein

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



>lcl|FitnessBrowser__HerbieS:HSERO_RS16715 HSERO_RS16715 sugar ABC
           transporter ATP-binding protein
          Length = 361

 Score =  315 bits (808), Expect = 9e-91
 Identities = 173/361 (47%), Positives = 229/361 (63%), Gaps = 3/361 (0%)

Query: 1   MTSVSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQI 60
           M SV +R +   FG+  ++  +++DI  GEF VL+G SGCGKSTLL  +AGL +++ G+I
Sbjct: 1   MASVQIRAVKKQFGSTQIIRGVDIDIADGEFTVLVGPSGCGKSTLLRMLAGLEEITGGEI 60

Query: 61  FIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEI 120
            I    V   +PKDR I MVFQ+YALYP MTV  N++F L +AK   A +++RVK+A++I
Sbjct: 61  LIGGTVVNNVQPKDRDIAMVFQNYALYPHMTVRDNMAFSLTLAKKDKAFVDERVKKAADI 120

Query: 121 LQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLH 180
           L +  LL R P +LSGGQRQRVA+GRA+VRD  VFLFDEPLSNLDAKLR ++R EIK LH
Sbjct: 121 LGLNQLLDRYPRQLSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRTEIKELH 180

Query: 181 QSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMN 240
           Q LK T IYVTHDQIEA+T+AD+I VM+ G+++Q   P+ +Y+ P NLFVAGFIGSP+MN
Sbjct: 181 QRLKTTSIYVTHDQIEAMTMADQIVVMRDGLVEQRGRPLDLYDYPANLFVAGFIGSPAMN 240

Query: 241 FFRGEVEPKDGRSFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEARDGEPTH 300
           F    +      + V           Y A  +   GQKV  G+RPEH+ +  A  G  T 
Sbjct: 241 FIPATLRRNATGAEVEFADGTRVPAPYGAALQGNDGQKVTYGVRPEHLSIGAAGQGIATK 300

Query: 301 QAVVDIEEPMGADNLLWLTFAGQSMSVRIAGQRRYPPGSTVRLSFDMGVASIFDAESENR 360
             VV   EP GAD  ++  F   S++     +  +  G  + L  D     +FDAES   
Sbjct: 301 VIVV---EPTGADTEVFSRFGDTSLTSIFRERHDFGAGDVIHLVPDHSRTHLFDAESGKS 357

Query: 361 L 361
           L
Sbjct: 358 L 358


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: 408
Number of extensions: 19
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: 361
Length adjustment: 29
Effective length of query: 332
Effective length of database: 332
Effective search space:   110224
Effective search space used:   110224
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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