GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Herbaspirillum seropedicae SmR1

Align ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized)
to candidate HSERO_RS02210 HSERO_RS02210 sugar ABC transporter ATP-binding protein

Query= reanno::WCS417:GFF2490
         (367 letters)



>FitnessBrowser__HerbieS:HSERO_RS02210
          Length = 372

 Score =  397 bits (1020), Expect = e-115
 Identities = 203/362 (56%), Positives = 260/362 (71%), Gaps = 2/362 (0%)

Query: 1   MANLKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGTI 60
           MA + I+NL K ++   +++ I+LE+ D EFVVFVGPSGCGKSTLLR+IAGLEE+S+G +
Sbjct: 1   MAAVSIRNLAKRYDDNEVMRDINLEIEDGEFVVFVGPSGCGKSTLLRMIAGLEEISDGDL 60

Query: 61  ELDGRDITEVTPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVDKKLVESKVSEAARI 120
           ++  R + EV  +KR +AMVFQ+YALYPHMS+  NM+F L +AG  K  +++ V  AA+I
Sbjct: 61  DIGARRMNEVPASKRGVAMVFQSYALYPHMSLYDNMAFGLKIAGKSKAEIDAAVQHAAKI 120

Query: 121 LELGPLLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLH 180
           L +  LL+RKP+ LSGGQRQRVAIGRAI R P +FLFDEPLSNLDAALRV+MRLE A+LH
Sbjct: 121 LHIDHLLDRKPRALSGGQRQRVAIGRAITRQPSVFLFDEPLSNLDAALRVKMRLEFAKLH 180

Query: 181 KELQATMIYVTHDQVEAMTLADKVVVLNSGRIEQVGSPLELYHQPANLFVAGFLGTPKMG 240
            +L+ TMIYVTHDQ+EAMTLADK+VVL+ GRIEQVGSP +LYH PAN FVAGF+G+PKM 
Sbjct: 181 DDLKTTMIYVTHDQIEAMTLADKIVVLSEGRIEQVGSPQQLYHHPANRFVAGFIGSPKMN 240

Query: 241 FLKGKVTRVESQSCEVQLDAGTLINLPLSGATLSVGSAVTLGIRPEHLEIASPGQTTLTV 300
           F+ G V  +++   +VQL  G L    + G+TL VG  VTLG+RPEHL IA  GQ  L  
Sbjct: 241 FIDGTVAAIQADGVQVQLPGGGLQWAAVDGSTLQVGQKVTLGVRPEHLNIAQ-GQAALQA 299

Query: 301 TADVGERLGSDTFCHVITANGE-PLTMRIRGDMASQYGETLHLHLDPAHCHLFDTDGVAV 359
                E LG  ++ +      E  L +R+   + + +G  L L  DPA CHLF  DG A+
Sbjct: 300 RCTALELLGDFSYLYAAYEGSEDALILRVPDSLDAPHGSVLPLAADPARCHLFGADGQAL 359

Query: 360 AR 361
            R
Sbjct: 360 PR 361


Lambda     K      H
   0.319    0.136    0.384 

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: 391
Number of extensions: 12
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: 367
Length of database: 372
Length adjustment: 30
Effective length of query: 337
Effective length of database: 342
Effective search space:   115254
Effective search space used:   115254
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